Have you tried:
- deactivating all plugins to see if this resolves the problem? If this works, re-activate the plugins one by one until you find the problematic plugin(s).
Yup. Was able to deactivate them all in the admin. Someone suggested go change the plug in folder name - I not only tried it on FTP but actually remoted onto the server and it would not grant me access to change the plug in name (access denise, in use...).
- switching to the default theme to rule out any theme-specific problems?
That was the first thing I did. And to rule that out I ran the install on another wordpress site I have (a test that is a stock install - only a child theme and no plug ins) and it bombed as well.
- re-uploading the wp-admin and wp-includes folders from a fresh download of WordPress?
I did one better - I killed EVERYTHING and downloaded and unzipped a fresh 3.1 to my server and put the files on the directory by hand.
Then on our WP test site we killed EVERYTHING including the database and did a 'from scratch' brand new install of 3.1 and had the same exact issues we had with the auto-updated site.
- Try re-saving your permalink structure or using the default structure at Settings/Permalinks in your admin panel. If WordPress cannot automatically edit the .htaccess file, it will provide manual instructions after saving.
-renaming your .htaccess to test.htaccess
I'm on a windows machine.