Well it should flag them as spam, but unlike the MS Outlook plug-in which moves them to the Spam folder, the anti-spam module can't work for 'all' the different email programs out there. It would effectively need to have a plug-in for each and every email client and that would add a high degree of complexity to the anti-spam module.
I have for many years used MailWasher Pro as my anti-spam and that operates outside of the email client and what it or I flag as spam is deleted from the email servers before downloading the remainder.
MailWasher downloads a small part (plain text, no attachments) to analyse for spam and when complete deletes the spam from the email server and calls your email client to download the remainder.
I think the problem with the avast anti-spam module is it is effectively trying to operate in conjunction with the avast Mail Shield.
I would agree that the thunderbird junk/anti-spam function is not very user friendly, I have only been using thunderbird for a couple of months and have never really had need of the TB junk/anti-spam when using MailWasher (and as such even if I have AIS I wouldn't have use for that either).