Hi, I upgraded from 3.01 to 3.2.1 on a multisite installation. I had difficulties with out of memory issues (128m php, 64meg WP) so I finally did a manual installation, which started working. I did a re-install and network updates from the admin panel and all seemed to work fine, no errors.
The main site looks and works fine in all respects, including administration, but all other sites appear to not be loading the default 2010 theme correctly (unformatted text, brief flash of the header image section and then it's gone, so no CSS), and trying to access their admin sections gives a 404 error. I tried making new sites and that works fine, except that they show the same issues.
I disabled and even removed all plugins (deleted them entirely) and reran the re-install and network updates repeatedly, and it comes through successfully every time, showing all sites updating.
I checked the .htaccess file and ensured it had the same rewrite rules as always, and didn't see any new .htaccess in the WP 3.2.1 download, so I'm guessing that's not the problem. I checked the database and the links to the blogs are also exactly as expected, so I have no idea what is up with this issue.
Has anyone any ideas as to what may be wrong? Any help would be greatly appreciated!