I have been having an issue when attempting to transfer animations to a new rig using HumanIK. The joints in the destination rig will flip around unpredictably when moving the source rig.
We made a ticket similar to this in the past, but we were told it was just a bug with maya LT. Since then we've updated to full Maya but it is still occurring.
I have looked into gimbal lock issues and nothing seems to work. The only thing that looks off to me is that the character joint orientations are strange (created with the Autodesk character generator so I assumed it should work correctly for this).
Any ideas why this might be happening? I have attached the mb file.