I think that, from reading the manual, you can import animation from an FBX character if it is not in the "biped" library internal to 3DXchange.

So..... Make your figure "not a biped". Add some extra limbs to the root, or something.

Another idea for using a standard biped might be to make sure your facial mocap bones are below the "Head" bone. Make the head nub at the top the head bone, or something. I'm guessing on this because anything above the head bone seems to be reserved.

Good luck!