I'm using several GMail accounts with Thunderbird and FireTray and FireTray counts every unread message twice because of their presence in "All Mail".
I do have "All Mail" selected as the archival location so, at least, I'd expect my intent to be made clear to FireTray by having "Archive" deselected in "Included special folders".
This happens with every version of FireTray I've ever used from 0.3.x (and possibly older) pre-ctypes versions right up through 0.4.1 from AMO and 2e65e07 in the themable-icons branch.
From my perspective, there are two bugs here:
The latter may or may not be soluble. You'd have to see whether GMail's IMAP implementation exposes any kind of message ID that's unique across different folders.
I get this error too, except I don't know about archiving.