I just noticed that this is still a problem with the beta2 release.
I installed it on a server and tried to create a user named "[email protected]" and point it to the directory /var/www/virtual/domain.tld/staff but when I or anybody else went to log in, it gave a "no active repository found for user" error.
So now it is happening with not only domain root access FTP accounts, but other accounts as well.
Is it just me that is having this problem? I'm installing it on a clean server so I don't know what I'm doing wrong...