It sounds to me like you have messed up your filters. If that is the case there is nothing anyone but you can do to correct that situation. DO you have a third party antivirus program? If yes have you created an exception in that product to prevent it scanning in the Thunderbird profile folder? I can see a situation where the actual file that holds your mail prefiltering is locked by the antivirus and therefore the move for a particular message is blocked so a latter filter get it. However, have you checked the filter log to see what is happening with those individual emails.