I'd appreciate advice on why Upgrade Site might not be working properly, and best course of action.
Following upgrade from 1.3.3 to 1.5.1 Upgrade Site appeared to run OK, but comments on pre-upgrade blogs don't appear under Site Admin/Comments, except for on the home blog. The number awaiting moderation is displayed, but that's all. They do appear for post-upgrade blogs.
Upgrade Site hasn't made some needed database changes. Pre-upgrade blogs have only two alternate keys in the wp_<id>_comments table; comment_approved and comment_post_ID. Post-upgrade blogs have two more; comment_approved_date_gmt and comment_date_gmt.
Trying again hasn't helped. All plugin files were removed during upgrade.
Also, table wp_blog_versions contains db_version values of 6125 for every blog (I upped the number from 6124 at some stage during 1.3.3 upgrade). It doesn't have entries for recent blogs (highest ID is currently 1094, but table doesn't contain values over 980). Sampling wp_<id>_options tables shows db_version is 6125 there too.
version.php is standard:
$wp_version = '2.5.1';
$wp_db_version = 7796;
$wpmu_version = '1.5.1';
Site is a subdirectory install and environment is Apache 2.0.55, Ubuntu, PHP V5.1.2 using CGI/1.1, My SQL 5.0.22
The database was created with WPMU 1.0RC4, and was using latin1 encoding which I changed to utf8 months after the upgrade. Apart from the Manage Comments issue, everything is working fine.
Usual advice on forcing an upgrade relies on upping the db_version in version.php to a higher value than that in the database - but it already is.
Similar symptoms have been discussed in a forum thread. That suggests changing the database tables, but that wouldn't give me confidence that something else hadn't been missed, or get db_version corectly set.
Thanks for taking the time to read this.