Yeah, I'm having similar problems with my map as well. The easiest thing to do is to paint the underlying terrain impassable. But that would render it impassable forever, and even if the building is destroyed units may walk through it.
I'm going to experiment with one thing that seems similar to this. If it works, I'll report.
The basic solution to this, I believe lies in MAP.INI. There must be some code to set a building collision on of off. INI experts?