I don't know how anything works here, so I don't know how useful my suggestions might be, but:
1. Mark threads as read only:
- when they are read
- when you click on "mark this forum as read"
- maybe add a "mark all forums as read" at the top level

or
2. Only mark them as read when the last login/access was more than 2 or 3 hours ago.

I would prefer the first one myself, with such a short timeout you can't assume that people have actually left just because they're logging in again.

Otherwise I have to read everything before I respond to anything, which is... not a bad idea, but not what I currently do. :)