Looks like somebody didn't read the UPGRADE doc...
Due to the database format change, you will want to do something like this when upgrading:
I read it and followed the directions and didn't see any problem for a couple days and then suddenly the spam level jumped substantially. Upon further investigation it looked like the bayes dbs had gotten corrupted and I was seeing low tok counts like the original poster had reported. Another friend saw this happen when he first upgraded, although I can't speak for his direction-following on the upgrade.
If I see more of this I'll try and isolate it and file an appropriately detailed bug report, but I don't think it's necessarily accurate to immediately write this off as user error.
-faisal