Log into your mysql database and run this query
select uid,gid from dbispconfig.mail_user where not uid=5000;
what is the result of the query?
also /var/vmail/domain.com has no +x group rights .. though i still think it's strange it doesn't work, try giving /var/vmail/domain.com +x on the group so:
chmod g+x /var/vmail/domain.com
If that solves your problem, then dovecot in some way must check the the gid rights as well.