I managed to get it working (at least temporarily) by deleting the symlink and then re creating it. Why that has worked I can't tell you, but the two user's I tested it on had previously been deleted off the system and recreated and still didn't work.
Current output of ls-al is:
lrwxrwxrwx 1 root root 33 2008-06-30 23:02 Maildir -> user/name.domain.com/Maildir
So I checked another domain where I haven't recreated the symlink and here's the problem. The ISPconfig generated symlink is
lrwxrwxrwx 1 root root 46 2008-06-30 16:23 Maildir -> /home/web7/user/user.domain.com/Maildir
Obviously the admin user has issues accessing the domain like that so can I edit any of the ISPconfig files to change how it creates a symlink? Or is there something else that I can do?