The problem is in the way the subforums are displayed. If they were displayed hierarchically, that would be great. Right now it is a matter of having to fiddle with check boxes to filter out other stuff. I think UI navigation is the key here.
I do agree that, no matter the topic, if it is about many instances of some topic, then separate threads are better than everything being co-mingled into a single thread. The sub-forum (or whatever grouping object it is) could hold the name of the topic and then the threads could be for each instance of that topic. I think bug-zilla type tracking is better for bugs too, but using that as an example, having a different thread per bug would be the aim.
In the current form of the forums, I think they need another layer under the top groupings and that is where the sub-groupings would be and then finally the threads within those sub-groupings. But we need a hierarchical way to navigate from the main list (with the main list showing the top level groupings and being able to expand them to drill down).