Amegpo can you explain the new slots to me? it sounds like these new slots are the cause of the armor/custom body problems
http://www.creationkit.com/UnequipItemSlot_-_Actor . Could have something to do with the problems, but this is only intended for armor slots, no body parts. So, unless there are two different very similar problems, I would say that the cause is other.
One thing though that is extremelly suspicious is the "Forces this actor to unequip all armor on the given slot." part. they say all armor not any armor, so, could be that the possibility to equip various items in the same slot is not part of the bug but a new feature.