I have tried gmail's iMap-interface and have gone back to the web interface. My tags where represented as folders, but on the same level as Inbox, so TB wouldn't update them; as I have set up several filters which sort my mail by tagging them, I do not see them until I manually update the folder.
Let's say I have one filter for all mails regarding donationcoder: the filter applies the tag "DC" and archives them. Now in TB I don't see a new mail in Inbox (because it's already in DC), nor do I see a new mail in DC unless I select that folder which updates it. I think it would work better if those folders where subfolders of Inbox, but I don't know for sure.
Maybe I need to disable gmail's filter and set them up in TB... I shall try and report back!