I got same problem described here: http://www.digitaltutors.com/forum/showthread.php?31792-Is-there-any-way-to-scale-a-skinned-model-and-freeze-transformations My rig and controllers have transformations on them, mainly the global control, that without them, would have my joints positioned incorrectly. This happened…
When I have parent transform issues like this I usually solve by transferring to a copy of the skeleton. Saved skin weights reapplied or most likely I will retarget the joint rotation onto the copied skeleton. ( zeroes still on my bind pose )…