For a long time, every so often I'd import a rig that is seemingly fit for mocap, that randomly gets disfigured when imported for tracking. Bones twisted, orientations backwards, scaling heightened. I wouldn't mind it if I new there was something wrong with the rigs themselves, but so far I have nothing to point to other than the software. I need this for production, so any help owuld be appreciated.

Hi
I believe the problem is linked to setting up a motion transfer profile for your rig. That is, a correspondence between joints of the model in Mocap Studio and your rig. For instance, on your second screenshot I see (by selection highlight) that your rig's right forearm is matched to model's hips.
You may send me your character if you wish. Then I'll try to set up a proper motion transfer profile for it or to identify other issues if any. You can send it to our tech support email if you don't want to share your rig in public.

I'm several months late, but it's still just as urgent. I can send you the files, but I'm 99% sure I targeted it correctly.
https://www.mediafire.com/file/ensv2pn5 ... i.rar/file
http://www.mediafire.com/file/r6sayfwfp ... a.dmx/file