Using dovecot 1.0.rc21, with quotas being stored in mysql, I have found that if the quota usage stored is negative, then when a message is given to dovecot deliver, the account is reports as being over quota. The squirrelmail quota usage plugin says that the quota is at around 40 million percent (I should have written down the exact number), though I don't know if that's squirrelmail or dovecot coming up with that number. At a guess, I'd say there's an unsigned int being used where the result can be signed.
I'm using MySQL 5, so for an easy workaround, I added a trigger that sets the quota usage to 0 if it goes less than 0. I could probably also set the field to unsigned int, but I haven't tested what mysql does if you try to change an unsigned int field such that it would be negative.
-- Marshal Newrock, Ideal Solution LLC http://www.idealso.com