On October 11, Mark Farmer reported a problem about not being able to see new mails. I'm running into the same issue. Even though cur/ and new/ contain messages, Dovecot reports that there aren't any.
This problem seemed to start happening in alpha3 (and persists in alpha4).
When I revert back to alpha2, the messages show up again.
It looks like a problem with the dovecot.index* files. When I delete them, alpha4 can serve up the mails just fine, and will in fact keep working for a little while. Eventually (within a few hours, although I'm not sure what causes it), dovecot thinks things are empty again.
Like Mark, I'm using Postfix.. I'm not sure if that has anything to do with the problem but I thought it'd be worth pointing out.
If there are any specific things you'd like me to do to try to pin down this problem, let me know.
Chris