For most of the simple animations I imported the ART skeleton in MotionBuilder and characterized it. Once the mocap animation is baked I then export as an FBX. The next step is, unfortunately for you, using the import mocap command.
I think we should focus on the FBX import dialog and this kind of options.
Can you import your baked mocap animation in an empty scene and check it? It should have only the animated skeleton. If not try to export again from MoBu using the export selection option. Then try again.
Let’s have a clean file before going into the problem