Thanks gr5. All great suggestions.
I eventually found it that it was, in fact, a blender issue. Blender is strange with holes. I had to "hide" certain objects in blender for the holes to be exported correctly.
I'm very interested in the other software you suggested. I'd just like to quickly check about a couple things:
What would you suggest for mac? I use a Silicon Mac, not a PC.
Is this software scriptable? My favorite part of Blender is that I can write python code that automates everything.