I'm having the same problem between Gnus (my primary client) and a couple of Thunderbirds I'm
having in auxiliary machines, all with imap. Although I cannot confirm it, I'd say that it is
the Thunderbirds that ignore the read flags from Gnus, or Gnus is not diligent enough to send
them promptly to the imap server. It is really annoying, but I don't have the time to isolate
who's fault is it.
Anybody else has more details?