>> Are you using LDA/LMTP to deliver messages to the inbox?
Not use LDA in dovecot,  i'm running  Dovecot with protocols imap pop3 lmtp

One thing, curious in accounts with problem with quota : 

i deleting dovecot index and  ran one force-resync  and him crashed and return segmentation fault

I thought the same could happen with the quota, leaving the count incomplete

This is just a possibility that I think might be

Thanks a Lot
Marcelo