The system that marks unread threads as bold has been a thorn in my side since day one. I have just completed a thorough investigation of these issues, and have deployed some changes that should address them.
There is one big caveat: in order to facilitate the transition from the old "unread" subsystem to the new subsystem, I've had to arbitrarily show the 10 most recent threads as "unread" for everyone, and to show everything else as "read" for everyone. This is a compromise that should pretty quickly work itself out.
Also, please note that I haven't touched the code that marks entire sub-forums ("Southern Miss," "Politics," etc.) as unread. I've only attempted to fix the "unread" logic for individual topics.
Any details about your user experience are more than welcome.