I realize that it's been a while since you posted. Did you ever figure this out? Are you using the latest mObject 1.3.2?
I'm guessing that your last thought about exporting the entire scene as a single mesh was the correct solution. Having that many editable objects was probably overwhelming mObject whereas a single mesh is really all you need. I don't know what 3D program was used to create that scene but getting whoever made it to export it as a single mesh might solve your problem.