When I make a change in my puppet's photoshop and come back to Character Animator, there is something out of place. It is a fixed and independent element. I go back to photoshop to remove the element saved in my document and put the image back in its place, it works for a while but if I go back to photoshop to make changes it always starts again.
I had a similar problem after I had modified the shape of an object. A quick fix is to go to Rig and select the object or group and drag it back into place. Of course, you'll have to do it again each time you save the file as the problem is persistant. The only fix I've found is rather unpleasant: use save as to make a copy of your original and import and rebuild the rigging.
Can you attach a .puppet file so I can take a look?
And if you're able to post a file, can you also post a list of steps to be able to reproduce the problem?
Sometimes unexpected things can happen if you change the actual canvas size of your Photoshop document, but other than that, nothing should positionally change when you make edits in PS.