WordPress MU

I'm not really sure how to describe this - so here it goes.

I have a wpmu install with ~400 blogs on it. Randomly tonight I noticed that clicking the posts from the main page failed to work. After some digging and head scratching, I discovered a sequence to correct the problem (on that particular blog) only.

1) Login to the admin interface on that blog
2) Click on the permalink settings option
3) That's it - the permalink settings page just needs to be loaded - not saved or anything

I later discovered that the direct links to the posts from the main page did work if I added "/blog" in the url after he site_url and before the 2009 in the permalink structure.

Does anyone have any idea what going on here or has anyone experienced this problem?

I've tracked this down further - and i've having to issues $wp_rewrite->flush_rules() on every blog. Somehow, the rules are not set right. What would cause all of the sub blogs to pickup the wp_rewrite site from the main blog??

Correct Rules:

[robots\.txt$] => index.php?robots=1
            [.*wp-atom.php$] => index.php?feed=atom
            [.*wp-rdf.php$] => index.php?feed=rdf
            [.*wp-rss.php$] => index.php?feed=rss
            [.*wp-rss2.php$] => index.php?feed=rss2
            [.*wp-feed.php$] => index.php?feed=feed
            [.*wp-commentsrss2.php$] => index.php?feed=rss2&withcomments=1
            [feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?&feed=$matches[1]
            [(feed|rdf|rss|rss2|atom)/?$] => index.php?&feed=$matches[1]
            [page/?([0-9]{1,})/?$] => index.php?&paged=$matches[1]
            [comments/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?&feed=$matches[1]&withcomments=1
            [comments/(feed|rdf|rss|rss2|atom)/?$] => index.php?&feed=$matches[1]&withcomments=1
            [comments/page/?([0-9]{1,})/?$] => index.php?&paged=$matches[1]
            [search/(.+)/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?s=$matches[1]&feed=$matches[2]
            [search/(.+)/(feed|rdf|rss|rss2|atom)/?$] => index.php?s=$matches[1]&feed=$matches[2]
            [search/(.+)/page/?([0-9]{1,})/?$] => index.php?s=$matches[1]&paged=$matches[2]
            [search/(.+)/?$] => index.php?s=$matches[1]
            [category/(.+?)/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?category_name=$matches[1]&feed=$matches[2]
            [category/(.+?)/(feed|rdf|rss|rss2|atom)/?$] => index.php?category_name=$matches[1]&feed=$matches[2]
            [category/(.+?)/page/?([0-9]{1,})/?$] => index.php?category_name=$matches[1]&paged=$matches[2]
            [category/(.+?)/?$] => index.php?category_name=$matches[1]
            [tag/(.+?)/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?tag=$matches[1]&feed=$matches[2]
            [tag/(.+?)/(feed|rdf|rss|rss2|atom)/?$] => index.php?tag=$matches[1]&feed=$matches[2]
            [tag/(.+?)/page/?([0-9]{1,})/?$] => index.php?tag=$matches[1]&paged=$matches[2]
            [tag/(.+?)/?$] => index.php?tag=$matches[1]
            [author/([^/]+)/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?author_name=$matches[1]&feed=$matches[2]
            [author/([^/]+)/(feed|rdf|rss|rss2|atom)/?$] => index.php?author_name=$matches[1]&feed=$matches[2]
            [author/([^/]+)/page/?([0-9]{1,})/?$] => index.php?author_name=$matches[1]&paged=$matches[2]
            [author/([^/]+)/?$] => index.php?author_name=$matches[1]
            [([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&day=$matches[3]&feed=$matches[4]
            [([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/(feed|rdf|rss|rss2|atom)/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&day=$matches[3]&feed=$matches[4]
            [([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/page/?([0-9]{1,})/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&day=$matches[3]&paged=$matches[4]
            [([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&day=$matches[3]
            [([0-9]{4})/([0-9]{1,2})/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&feed=$matches[3]
            [([0-9]{4})/([0-9]{1,2})/(feed|rdf|rss|rss2|atom)/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&feed=$matches[3]
            [([0-9]{4})/([0-9]{1,2})/page/?([0-9]{1,})/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&paged=$matches[3]
            [([0-9]{4})/([0-9]{1,2})/?$] => index.php?year=$matches[1]&monthnum=$matches[2]
            [([0-9]{4})/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?year=$matches[1]&feed=$matches[2]
            [([0-9]{4})/(feed|rdf|rss|rss2|atom)/?$] => index.php?year=$matches[1]&feed=$matches[2]
            [([0-9]{4})/page/?([0-9]{1,})/?$] => index.php?year=$matches[1]&paged=$matches[2]
            [([0-9]{4})/?$] => index.php?year=$matches[1]
            [[0-9]{4}/[0-9]{1,2}/[0-9]{1,2}/[^/]+/attachment/([^/]+)/?$] => index.php?attachment=$matches[1]
            [[0-9]{4}/[0-9]{1,2}/[0-9]{1,2}/[^/]+/attachment/([^/]+)/trackback/?$] => index.php?attachment=$matches[1]&tb=1
            [[0-9]{4}/[0-9]{1,2}/[0-9]{1,2}/[^/]+/attachment/([^/]+)/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?attachment=$matches[1]&feed=$matches[2]
            [[0-9]{4}/[0-9]{1,2}/[0-9]{1,2}/[^/]+/attachment/([^/]+)/(feed|rdf|rss|rss2|atom)/?$] => index.php?attachment=$matches[1]&feed=$matches[2]
            [[0-9]{4}/[0-9]{1,2}/[0-9]{1,2}/[^/]+/attachment/([^/]+)/comment-page-([0-9]{1,})/?$] => index.php?attachment=$matches[1]&cpage=$matches[2]
            [([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/([^/]+)/trackback/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&day=$matches[3]&name=$matches[4]&tb=1
            [([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/([^/]+)/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&day=$matches[3]&name=$matches[4]&feed=$matches[5]
            [([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/([^/]+)/(feed|rdf|rss|rss2|atom)/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&day=$matches[3]&name=$matches[4]&feed=$matches[5]
            [([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/([^/]+)/page/?([0-9]{1,})/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&day=$matches[3]&name=$matches[4]&paged=$matches[5]
            [([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/([^/]+)/comment-page-([0-9]{1,})/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&day=$matches[3]&name=$matches[4]&cpage=$matches[5]
            [([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/([^/]+)(/[0-9]+)?/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&day=$matches[3]&name=$matches[4]&page=$matches[5]
            [[0-9]{4}/[0-9]{1,2}/[0-9]{1,2}/[^/]+/([^/]+)/?$] => index.php?attachment=$matches[1]
            [[0-9]{4}/[0-9]{1,2}/[0-9]{1,2}/[^/]+/([^/]+)/trackback/?$] => index.php?attachment=$matches[1]&tb=1
            [[0-9]{4}/[0-9]{1,2}/[0-9]{1,2}/[^/]+/([^/]+)/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?attachment=$matches[1]&feed=$matches[2]
            [[0-9]{4}/[0-9]{1,2}/[0-9]{1,2}/[^/]+/([^/]+)/(feed|rdf|rss|rss2|atom)/?$] => index.php?attachment=$matches[1]&feed=$matches[2]
            [[0-9]{4}/[0-9]{1,2}/[0-9]{1,2}/[^/]+/([^/]+)/comment-page-([0-9]{1,})/?$] => index.php?attachment=$matches[1]&cpage=$matches[2]
            [([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/comment-page-([0-9]{1,})/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&day=$matches[3]&cpage=$matches[4]
            [([0-9]{4})/([0-9]{1,2})/comment-page-([0-9]{1,})/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&cpage=$matches[3]
            [([0-9]{4})/comment-page-([0-9]{1,})/?$] => index.php?year=$matches[1]&cpage=$matches[2]
            [.+?/attachment/([^/]+)/?$] => index.php?attachment=$matches[1]
            [.+?/attachment/([^/]+)/trackback/?$] => index.php?attachment=$matches[1]&tb=1
            [.+?/attachment/([^/]+)/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?attachment=$matches[1]&feed=$matches[2]
            [.+?/attachment/([^/]+)/(feed|rdf|rss|rss2|atom)/?$] => index.php?attachment=$matches[1]&feed=$matches[2]
            [.+?/attachment/([^/]+)/comment-page-([0-9]{1,})/?$] => index.php?attachment=$matches[1]&cpage=$matches[2]
            [(.+?)/trackback/?$] => index.php?pagename=$matches[1]&tb=1
            [(.+?)/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?pagename=$matches[1]&feed=$matches[2]
            [(.+?)/(feed|rdf|rss|rss2|atom)/?$] => index.php?pagename=$matches[1]&feed=$matches[2]
            [(.+?)/page/?([0-9]{1,})/?$] => index.php?pagename=$matches[1]&paged=$matches[2]
            [(.+?)/comment-page-([0-9]{1,})/?$] => index.php?pagename=$matches[1]&cpage=$matches[2]
            [(.+?)(/[0-9]+)?/?$] => index.php?pagename=$matches[1]&page=$matches[2]

Incorrect rules:

[robots\.txt$] => index.php?robots=1
            [.*wp-atom.php$] => index.php?feed=atom
            [.*wp-rdf.php$] => index.php?feed=rdf
            [.*wp-rss.php$] => index.php?feed=rss
            [.*wp-rss2.php$] => index.php?feed=rss2
            [.*wp-feed.php$] => index.php?feed=feed
            [.*wp-commentsrss2.php$] => index.php?feed=rss2&withcomments=1
            [feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?&feed=$matches[1]
            [(feed|rdf|rss|rss2|atom)/?$] => index.php?&feed=$matches[1]
            [page/?([0-9]{1,})/?$] => index.php?&paged=$matches[1]
            [comments/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?&feed=$matches[1]&withcomments=1
            [comments/(feed|rdf|rss|rss2|atom)/?$] => index.php?&feed=$matches[1]&withcomments=1
            [comments/page/?([0-9]{1,})/?$] => index.php?&paged=$matches[1]
            [search/(.+)/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?s=$matches[1]&feed=$matches[2]
            [search/(.+)/(feed|rdf|rss|rss2|atom)/?$] => index.php?s=$matches[1]&feed=$matches[2]
            [search/(.+)/page/?([0-9]{1,})/?$] => index.php?s=$matches[1]&paged=$matches[2]
            [search/(.+)/?$] => index.php?s=$matches[1]
            [blog/category/(.+?)/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?category_name=$matches[1]&feed=$matches[2]
            [blog/category/(.+?)/(feed|rdf|rss|rss2|atom)/?$] => index.php?category_name=$matches[1]&feed=$matches[2]
            [blog/category/(.+?)/page/?([0-9]{1,})/?$] => index.php?category_name=$matches[1]&paged=$matches[2]
            [blog/category/(.+?)/?$] => index.php?category_name=$matches[1]
            [blog/tag/(.+?)/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?tag=$matches[1]&feed=$matches[2]
            [blog/tag/(.+?)/(feed|rdf|rss|rss2|atom)/?$] => index.php?tag=$matches[1]&feed=$matches[2]
            [blog/tag/(.+?)/page/?([0-9]{1,})/?$] => index.php?tag=$matches[1]&paged=$matches[2]
            [blog/tag/(.+?)/?$] => index.php?tag=$matches[1]
            [blog/author/([^/]+)/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?author_name=$matches[1]&feed=$matches[2]
            [blog/author/([^/]+)/(feed|rdf|rss|rss2|atom)/?$] => index.php?author_name=$matches[1]&feed=$matches[2]
            [blog/author/([^/]+)/page/?([0-9]{1,})/?$] => index.php?author_name=$matches[1]&paged=$matches[2]
            [blog/author/([^/]+)/?$] => index.php?author_name=$matches[1]
            [blog/([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&day=$matches[3]&feed=$matches[4]
            [blog/([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/(feed|rdf|rss|rss2|atom)/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&day=$matches[3]&feed=$matches[4]
            [blog/([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/page/?([0-9]{1,})/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&day=$matches[3]&paged=$matches[4]
            [blog/([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&day=$matches[3]
            [blog/([0-9]{4})/([0-9]{1,2})/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&feed=$matches[3]
            [blog/([0-9]{4})/([0-9]{1,2})/(feed|rdf|rss|rss2|atom)/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&feed=$matches[3]
            [blog/([0-9]{4})/([0-9]{1,2})/page/?([0-9]{1,})/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&paged=$matches[3]
            [blog/([0-9]{4})/([0-9]{1,2})/?$] => index.php?year=$matches[1]&monthnum=$matches[2]
            [blog/([0-9]{4})/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?year=$matches[1]&feed=$matches[2]
            [blog/([0-9]{4})/(feed|rdf|rss|rss2|atom)/?$] => index.php?year=$matches[1]&feed=$matches[2]
            [blog/([0-9]{4})/page/?([0-9]{1,})/?$] => index.php?year=$matches[1]&paged=$matches[2]
            [blog/([0-9]{4})/?$] => index.php?year=$matches[1]
            [blog/[0-9]{4}/[0-9]{1,2}/[0-9]{1,2}/[^/]+/attachment/([^/]+)/?$] => index.php?attachment=$matches[1]
            [blog/[0-9]{4}/[0-9]{1,2}/[0-9]{1,2}/[^/]+/attachment/([^/]+)/trackback/?$] => index.php?attachment=$matches[1]&tb=1
            [blog/[0-9]{4}/[0-9]{1,2}/[0-9]{1,2}/[^/]+/attachment/([^/]+)/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?attachment=$matches[1]&feed=$matches[2]
            [blog/[0-9]{4}/[0-9]{1,2}/[0-9]{1,2}/[^/]+/attachment/([^/]+)/(feed|rdf|rss|rss2|atom)/?$] => index.php?attachment=$matches[1]&feed=$matches[2]
            [blog/[0-9]{4}/[0-9]{1,2}/[0-9]{1,2}/[^/]+/attachment/([^/]+)/comment-page-([0-9]{1,})/?$] => index.php?attachment=$matches[1]&cpage=$matches[2]
            [blog/([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/([^/]+)/trackback/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&day=$matches[3]&name=$matches[4]&tb=1
            [blog/([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/([^/]+)/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&day=$matches[3]&name=$matches[4]&feed=$matches[5]
            [blog/([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/([^/]+)/(feed|rdf|rss|rss2|atom)/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&day=$matches[3]&name=$matches[4]&feed=$matches[5]
            [blog/([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/([^/]+)/page/?([0-9]{1,})/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&day=$matches[3]&name=$matches[4]&paged=$matches[5]
            [blog/([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/([^/]+)/comment-page-([0-9]{1,})/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&day=$matches[3]&name=$matches[4]&cpage=$matches[5]
            [blog/([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/([^/]+)(/[0-9]+)?/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&day=$matches[3]&name=$matches[4]&page=$matches[5]
            [blog/[0-9]{4}/[0-9]{1,2}/[0-9]{1,2}/[^/]+/([^/]+)/?$] => index.php?attachment=$matches[1]
            [blog/[0-9]{4}/[0-9]{1,2}/[0-9]{1,2}/[^/]+/([^/]+)/trackback/?$] => index.php?attachment=$matches[1]&tb=1
            [blog/[0-9]{4}/[0-9]{1,2}/[0-9]{1,2}/[^/]+/([^/]+)/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?attachment=$matches[1]&feed=$matches[2]
            [blog/[0-9]{4}/[0-9]{1,2}/[0-9]{1,2}/[^/]+/([^/]+)/(feed|rdf|rss|rss2|atom)/?$] => index.php?attachment=$matches[1]&feed=$matches[2]
            [blog/[0-9]{4}/[0-9]{1,2}/[0-9]{1,2}/[^/]+/([^/]+)/comment-page-([0-9]{1,})/?$] => index.php?attachment=$matches[1]&cpage=$matches[2]
            [blog/([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/comment-page-([0-9]{1,})/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&day=$matches[3]&cpage=$matches[4]
            [blog/([0-9]{4})/([0-9]{1,2})/comment-page-([0-9]{1,})/?$] => index.php?year=$matches[1]&monthnum=$matches[2]&cpage=$matches[3]
            [blog/([0-9]{4})/comment-page-([0-9]{1,})/?$] => index.php?year=$matches[1]&cpage=$matches[2]
            [.+?/attachment/([^/]+)/?$] => index.php?attachment=$matches[1]
            [.+?/attachment/([^/]+)/trackback/?$] => index.php?attachment=$matches[1]&tb=1
            [.+?/attachment/([^/]+)/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?attachment=$matches[1]&feed=$matches[2]
            [.+?/attachment/([^/]+)/(feed|rdf|rss|rss2|atom)/?$] => index.php?attachment=$matches[1]&feed=$matches[2]
            [.+?/attachment/([^/]+)/comment-page-([0-9]{1,})/?$] => index.php?attachment=$matches[1]&cpage=$matches[2]
            [(.+?)/trackback/?$] => index.php?pagename=$matches[1]&tb=1
            [(.+?)/feed/(feed|rdf|rss|rss2|atom)/?$] => index.php?pagename=$matches[1]&feed=$matches[2]
            [(.+?)/(feed|rdf|rss|rss2|atom)/?$] => index.php?pagename=$matches[1]&feed=$matches[2]
            [(.+?)/page/?([0-9]{1,})/?$] => index.php?pagename=$matches[1]&paged=$matches[2]
            [(.+?)/comment-page-([0-9]{1,})/?$] => index.php?pagename=$matches[1]&cpage=$matches[2]
            [(.+?)(/[0-9]+)?/?$] => index.php?pagename=$matches[1]&page=$matches[2]