After not even thinking about the QBSP problem for several weeks, I got the urge to try again. This time I had a little more luck. Bengt has been working on some modified tools for a little while and I decided to check out his version of TreeBSP (treeqbspbjp), which uses double precision floats (more accurate). The extra precision solved some of the problems, but not quite all.
So, with a little more poking around I found a problem with the code that generates the clip hulls (used for collision checking) which has been in the tools even since id's original version. Now, you know how anytime you try to get creative with your brushes, almost always you end up with places where the scenery goes non-solid? Well, I think I've got it fixed. Damn, I feel proud.
I've sent off the changes to Bengt and I'm just waiting for him to get back to me. At this stage it's not really worth me releasing my own Qbsp since Bengt's been working on his for a while, so I'll let him take care of releasing an updated version. Of course if he decides not to for some reason then I'll upload something myself.
Oh, and yes, this means I'm going to start working on my new map again. =)