I reinstalled all from scratch with the install guide (ubuntu 9.04), and tried it with all the default directories.
I still have the same problem, it seems postfix doesn't check if a user exists when receiving mail and creates all the maildirs.
Could it be that postfix doesn't connect to the mysql database? all the /etc/postfix/mysql_virtual_*.cf generated by ispconfig seem correct. How could I see if postfix correctly gets the virtual user data?