Thunderbird filters do not function reliably
The Junk filter and all of the other filters I've set up do not work reliably. When I check mail, the filters work on some, but not all, of the incoming messages. As a partial workaround, I've been using the Folder Filters Button extension. Every time I receive a batch of mail, I click the button, and that seems to trigger the filters to act on the messages it missed (most of them, anyway). This has been going on ever since I started using Thunderbird a few years ago. The Junk filter works better than it did at first, but that's to be expected, and it still doesn't catch as much spam as others I've used previously with other email clients.
Every once in awhile, the unreliability gets to me, but I've never been able to do anything to improve the situation. I've renamed the Thunderbird shortcut to Blunderturd, as this seems accurate, and it keeps me from getting as angry when it screws up.
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filter work on the inbox when receiving new mail, so if the new mail is in say "important" then the filter will not see it.
All of my filters are set to work when receiving new mail (which means they're looking only at the inbox). In many instances, they'll work correctly on some messages but not others, even though all the messages in question meet one or more of the rules I've set up. It's not unusual for one message from, e.g., The Washington Post, to be acted on by the filter while another message from the same sender is ignored, even though both were received during the same download, and the filter was set to look only at the from field. In other words, there was effectively no difference between the two messages, as defined by the filter rules, but one was moved to the correct destination folder while the other was ignored. This happens several times every day.
Some issues I have seen over the years for filter reliably all basically come down to contention for access to the mail in the folder.
So with that in mind, make sure you keep your inbox small and compact it regularly so the storage file can shrink. Small files are processed more quickly that large files.
Create an exception in your anti virus product for the Thunderbird profile folder. Having it scanning the mail file while Thunderbird is adding items and removing them is a primary source of this contention.