I take it back. In my case, the problem was due to courier-imap being
configured to only watch INBOX for changes. This setting:

IMAP_CHECK_ALL_FOLDERS=1

in /etc/courier/imapd fixes this. So in many cases, this problem may not
be related to thunderbird, but to the IMAP server being thrifty.

-- 
New mail is not noticed in IMAP subfolders
https://bugs.launchpad.net/bugs/106730
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