Cannot login directly into user account - first have to login as administrator
We've seen this behavior before when we migrate a user account onto a computer that already has FileVault disk encryption enabled, because the new user's login password isn't eligible to decrypt the disk at boot time. 

We resolve it in that case by bringing up the Security preference pane, which contains a warning that not all users are eligible to decrypt the disk, and steps you through fixing it (by providing the additional user's login password). 

I'm not sure if this also applies to symlinked home directories, but it's the first thing I'd check.