10.8.2 and Safari 6.0.2 on Mac with the same issue.
Till yesterday autofill was working, since this morning it's not working anymore on certain websites.
Also a huge number of passwords have disappeared from keychain.
Furthermore Safari is not offering saving the username/password for sites whose entries are missing from keychain.
Websites where autofill is not working anymore have no autofill tag in html at all.
Here's what helped:
- close all apps
- delete the 'com.apple.Safari' folder from ~/Library/Caches/...
- I've restored the users 'login.keychain' from a Time Machine backup
you can find it here: Macintosh HD/Users/username/Library/Keychain/...
logout and login
Voila it's working again!