Since I don't have a scene in question and can't check it, I would suggest you to take a look at two possible culprits:
1. NodesConstraints all that is related to this character, their head, etc.
2. KKPE (select a problematic character, right-click on KKPE button, Bones) and check there any changes with the head.
Does this happen after the SD load or after starting timeline or after changing the character?