Ok. Found the culprit. AVG Tuneup.
I was playing with MailWasher and trained it. Closed Mailwasher. Re-opened it. Everyone good. Then...
Started AVG Tuneup. Activated manual maintenance which cleaned all sorts of things it thinks are;
1. Broken registry entries
2. Broken shortcuts
3. System junk
I think AVG Tuneup thinks anything in C:\Users\[username]\AppData\Roaming\Firetrust\MailWasher\cache\crypto is system junk because it decided to delete the ENTIRE directory. MailWasher was still running at the time so I can tell there aren't any locks on those files. I specifically added .0010 and 00.11 files to the monitor but AVG TuneUp deleted all the files in the crypto directory regardless.
When I closed MailWasher and re-opened it, all email was reset back to 0 spam weighting. I'll report a bug to AVG and get it sorted.
