The problems extend well past Windows/IIS platforms. My Ubuntu/Apache site had been through numerous automatic upgrades dating back to well before 3.0. Even the 2.x to 3.0 auto update went smoothly.
The 3.1 upgrade splattered it and it’s still down. Attempts at manual upgrades have also failed, and I’ve found nothing in these forums that has been helpful. It was running the latest version of the Atahualpa theme, so it can’t be blamed on an “old” theme.
I’m about to try a fresh 3.1 install and I guess I’ll rebuild the site by picking all the old articles out of the database backups by hand.
This is truly ugly, and has severely lowered my confidence in WordPress as a platform. I have another half dozen sites to deal with, but they’re going to stay on 3.0.5 until I’m absolutely sure I understand what’s going so terribly wrong.
Fixing this appears not to be much less work than moving to a whole new platform. The WordPress folks really should have a tutorial page somewhere with a step-by-step how-to on doing a forensic manual restoration.
I’ll report back if I learn anything useful doing the rebuild.