Tell me about it. I've gone around and around with them trying to explain that templates do not control how the software runs and that they just control the look and feel of the forums.
The only thing I can think of is they may be getting confused because the default links for returning to the forum indexes are no longer there. I even compared their accounts to mine as far as how they are configured for viewing the forums and they were identical to mine. Because of that login as bug in 6.4.1 I can't even log on as a user to check it for myself..sigh.
Let me put yours back online and you can have a look through the forums and see if you think they are functioning properly.