Message filltering doesn't always work!

Question

I recently installed Thunderbird on a new computer, and copied the relevant directories than contained all the messages/account information from my old PC's Thunderbird installation to my new one. I did have to re-enter the account passwords, but after that all seemed to be working OK.
I have now noticed that some of the automatic message filtering that I had previously set up doesn't work and that the messages are left in the inbox. If I 'Run filters on folder' then the filters work, and the messages are moved to the correct folders accordingly.
FYI, I have 10 Mail accounts, all using POP. One of the accounts has its own dedicated inbox, all the others use the local folders inbox. (This dedicated inbox accounts filters only seem to work manually). Of the remaining 9 accounts, one is filtered by it's account name, the other 8 are filtered via the Local Folders filter. I have 294 filters in total.
All filters have the 'Manually Run' and 'Getting New Mail' tick box's checked and 'Filter before Junk Classification'.
I would have linked my problem with the Forum Question 'If I apply mail filters for message body , the filters stop applying automatically', however my problem appears to be random, and doesn't just apply to message body filters.
Has this problem been caused by the transfer of the accounts from one computer to another, or has this transfer just shown up a bug?
Am I likely to have to Identify which of the filters aren't working and have to re-enter them? (With 294 filters with a potential problem, this would take ages!). And would this cure the problem?

Answer 1

ok some background and some ideas.
Compact all folders [File menu (alt+F) Compact Folders]
Thunderbird stores all mail in a single files per folder, as these files get parger something functions just don't work.
Exclude the profile folder from on access scanning in your anti virus package and see if that helps. The getting of mail requires the update of the underlying MBOX files for each folder affected by that mail. If the anti virus is locking the files for scanning while Thunderbird is indexing and filtering the result can be unpredictable.
Thinking about the software you have installed, is there anything else that might be scanning file when they are accessed (MAlware detectors, keystroke monitors, net nanny type content filters etc)