A day ago, I tried to install WP Super Cache onto a perfectly working mu2.7 subdomain setup installed in root. The WPSC install worked, but I started noticing images appearing as broken links in some, then all blogs. I Determined, with the help of my host, that I had some incorrect ownership/permissions settings that were probably brought to light by the cache software. So we removed all the cache stuff and tried to take care of the permissions - perhapse too quickly - and managed to have to correct ourselves 2-3 times. (PHP 5.2.8 now verified file by file that directories are now 755 and files are 644)
The primary thing we were seeing with some of our improper repairs was that every post from all blogs went to a 404, even though the posts appeared as expected on the front page of the blogs, category lists, and feeds. But if you click on a post link, 404 every time. We believe the ownership/permissions stuff is correct now, but the final trick we had to do to fix the existing blogs was to revert the permalinks for each blog to the default setting then back to the /%postname%/ custom structure I have set up as the new account default. THEN all the posts in that blog worked fine.
The remaining issue I have is still a serious one: All *newly* created blogs have the 404 for all posts including the "Hello World". The set-up process works like a charm including email verification etc. Adding a new post shows no problems, URLs are correct, Pages work fine, but clicking on Posts always goes 404. The permalink flip trick still works on these.
Host says nothing is in the error logs. They did a repair on database which coughed up errors, but there are none now. I reinstalled the wpmu2.7 files overwriting the existing, then did an "Upgrade" from the admin - just in case. The script ran happily, but to no effect.
I asked my host to confirm that my current server settings for Apache, DNS, and PHP still match this setup doc (still waiting for result of that check):
http://trac.mu.wordpress.org/browser/trunk/README.txt
You can see the result of a new blog setup here:
http://captaincrunch.bestagentblogs.com/
Feel free to whip up your own. It'll look the same.
I freely admit that I am a hack and pushing the envelope of my skills here, so hopefully I'm just missing something that is obvious to the talented and experienced folks here.
TIA