I have an IMAP account with multiple folders in it, which each receive email directly. It seems like Thunderbird expects all messages to come into INBOX and be filtered into folders from there, but my email server pre-filters messages into folders. The consequence of this is that to be truly sure I have no email, after I manually select "Get All New Messages" ... I need to open every folder, or at least quickly run through each folder by selecting INBOX and using my down arrow-key to select each folder, which triggers a refresh of that folder. Only once the folders are manually refreshed by me selecting them, are new message counts shown. And there is a several-second delay for this, each time. Automatically checking and refreshing each folder on an IMAP account seems appropriate, at least as a configuration option, if not by default.

per http://kb.mozillazine.org/Mail_and_news_settings