Animation and Rigging Tools: FAQ, Known Issues and Feature Roadmap

I’m guessing the rig that the motion is being imported onto is the mannequin itself? So the skeletons (positions and all) are entirely aligned?

Some possible things to try:

Did you check your curves on the baked mannequin skeleton after to make sure there was no weird euler flips? Maybe run an euler filter on that skeleton before exporting.
Import mocap to FK, and then use match over frame range to match the IK to the FK.

Let me know if either of those works for you!