[support] upgrade to 4.6.5 broke mysql db

I upgraded a drupal site to 4.6.5 (it was 4.6.2) and now the database hass something wrong with it. I upgraded to 4.6.4 first, and ran the update scripts. I then upgraded to 4.6.5 and ran the update scripts (again)--I may have run the same update scripts twice, despite the warning not to, though there is no indication of what kind of problem this is supposed to cause.

The database still has all the data (I can browse the entries and see the most recent ones) but the website simply displays "Page Not Found" for most pages. It will load the correct theme though, and I can see the log page (http://frazer.rice.edu/nano-test/index.php?q=admin)... but that's it.

Anyone recognize what's gone wrong? ck