Yes it's definitely that the joint centers in the face are repositioned when that thumb morph is dialed in. I will try to get an update out as soon as I can.

In the meantime, what you can do is zero the figure so that all morphs are zeroed. Then dial in ONLY that GMThumb morph. Open the menu to the side of that morph in the Parameters Palette, and choose Match Centers to Morph. That will move the joint centers in the thumb to the correct position, but it will also snap the control chips in the head back to where they are supposed to be.

Thanks for pointing it out! Somehow that one slipped through.