I'm getting a strange bug, may be related. I have 14 Layer comps using visibility only. I updated one (intending to do all eventually) to use position as well. Without having done anything else (no moving ANYTHING), a few of the layers in some of the other comps have jumped around
This issue is caused specifically by using "Transform" (Command T) to move any objects from one position to another. You can move by the arrow keys. You can move by clicking and dragging but you CAN NOT use "Transform" to move anything in layer comps for positioning purposes.