I think I might have worked out the problem.
For other domains everything is under /home/domain/user/userid/Maildir/
but for this one it seems to create a new user thus: /home/domain/user/userid/user/userid/Maildir
The email is being delivered to /home/domain/user/userid/Maildir/new as it should be but it's connecting to the above extra directory which has nothing in. I'm not sure why this is as the other two accounts on that domain are set up properly as are the accounts on other domains.
I've tried adding a brand new user - this is set up correctly but still can't receive email via POP or IMAP