I had the same problem, with the master account and 3 mailboxes not showing up in CMM. I used the info found here to fix it.
The problem was $homedir/etc/$domain/passwd had the wrong path listed, and the GIDs were also showing as "-1". I created a mailbox then reviewed passwd again, and that gave me the proper GID and it showed the right path. I think the bad path came from when this account was imported from a Plesk server.
Hope this helps someone (or helps me when I come looking for answers again when I see this happen 3 years from now LOL)