I found out what was wrong.
I had already moved all my emails to the new format, it was sending with no problems but the emails i received were being sent to the default folder (/var/vmail) while i wanted them to go to somewhere else (/mail).
In the main.cf file on /etc/postfix two parameters were missing:
mail_spool_directory = /mail
home_mailbox = Maildir/
Once i added those the emails started to go to the correct directory.