Anyone seen this before? http://www.youtube.com/watch?v=fBE0DdX10_k

Not sure why, tried on multiple maps.

This happens to me every time I try to subtract. It just screws up the entire map. I don't think they changed how it worked since waw so it might just be a bug.

that is meant to be used in prefabs only

The only CSG mode that I would even recommend using is the hollow option. And I would use that only for creating a skybox. The other options always messed with my map file on WaW and would even mess things up for me when making Source engine maps as well.