I found a weird Thunderbird bug that sounds similar to this, so I'll describe it. It affected the Windows version of Thunderbird, not the Mac (didn't have a chance to test out the Linux version).
I had migrated from Courier to Dovecot. Courier had things in the INBOX namespace, and I got rid of that via the courier2dovecot script. I had people running Thunderbird on Windows adjust their namespace and close Thunderbird, then delete their IMAP cache. Then they restarted.
What Thunderbird then did was instead of using the Trash folder that was not in the INBOX namespace, it instead re-created the Trash folder as a subfolder of INBOX (Drafts and Sent did not have this problem). It also added a subscription to this folder. Both the Trash folders now (the one as a subfolder of Inbox and the one that wasn't) had the "trash" icon in Thunderbird, but Trash went to the one that was the subfolder of Inbox.. Attempting to go into the Thunderbird settings and change which of the two it was using did not help.
To fix this I had to have people close Thunderbird and delete their IMAP cache again. On the server side, I then had to rm -rf the INBOX.Trash folder in their account, and manually edit their subscriptions file to get rid of the extra INBOX.Trash entry. When they fired up Thunderbird again, it would start using the correct Trash folder.
IIRC this was the behavior on Thunderbird 1.5. On 1.0 I believe it did the same thing but didn't re-add the INBOX.Trash folder to subscriptions (again, IIRC...it was a bit ago and I've tried to forget this nightmare). Just another day in the life, and why I use KMail. It may crash more, but it ain't crazy.
--Jeff