OH!

 I should also mention near the beginning I was experimenting with the Poser morphing brush (which I've never done before) to try and smooth some joints. I ended up zeroing the morph and not using it, but could that be a part of the problem?

 And another weird thing.. the second loop that I load, it plays fine.. but then when it gets to the start of the original loop, jitteryness.

 Another note, If I click "undo" immediately after loading the second loop, going back to one loop - the hands/feet are all mangled and broken. 

Grr, Poser is driving me bonkers.