Hey binary1!
I'm not an expert in either 3D Studio or it's MOCAP functions, but however you do the animation of your character(s), in the end it has to be keyframed and properly set according to this in the Panda exporter.
Therefore if the mentioned MotionBuilder relies on non-standard methods for animation, you need to somehow "convert" that into a normal keyframed animation, where the bones are properly moved. I think at least. Seems like the most technically logical answer.