I know that this is a somewhat old thread but I do have some useful input.
Basically, this seems to be a Thunderbird problem (or at least an interaction problem between Thunderbird and Dovecot).
Before Thunderbird version 3 there wasn't a problem, the mailbox within Thunderbird would sync correctly. As of version 3 they seem to have changed their mailbox header list caching code and it gets horribly confused when mails disappear from the mailbox without it doing so. The only way to fix the view within the program is the rebuild the (Thunderbird) index.
This is not the only problem TB3 has with Dovecot. Quite often if there are large attachments TB doesn't fully load the attachments (and sometimes not even the mail itself). I've found changing TBs setting so that it only uses one connection to the server rather than the default 5 helps mitigate this.
I'm not sure why TB3 has such a hard time when talking to Dovecot as no other clients have any difficulty and TB2 never did.
Steve
P.S. Our system is a Solaris 10 x86 box running Dovecot 1.2.x with Maildir++ folders.
IT Systems Administrator, E-Mail:- steve@earth.ox.ac.uk Department of Earth Sciences, Tel:- +44 (0)1865 282110 Oxford University, South Parks Road, Oxford, UK. Fax:- +44 (0)1865 272072