I'll play around with it for a bit and see if I can figure anything out. If I reimport the MDB to Blender I get the same thing back, so at least I know it isn't a problem with the import/export script.
I'll try playing around with it and see what I can figure out. I've been basing what I've done off of tupoun's stuff, but I don't really know if he worked in Blender or not. Rearranging the walkmesh as follows didn't seem to do the trick (although it is lower poly so I might keep this).

As it stands the walkmesh is contained (vertically) within the C2 and C3 boxes, and the C3 box is contained within the C2 box (this is not consistent with tupoun's models, where the relative sizes of these three vary from model to model). The C2 box is all enclosing, while the C3 box has an open floor, again following tupoun's example.
I've gotta say, what -really- baffles me is that I do get C3 data, but -just- on those illuminated windows, which are one whole part of the model.
EDIT: Woooo, I finally got this working! I have no idea why, but I did it by copying everything into a new blend file. Blender was doing something odd and I have no idea what.