Just found out why the game seems to be doing this:
When you load a troll it's only loading its appearance, the data is kinda there just like a ghost, but it's not really there, to the game itself?
I found that a way to fix it is to click new troll, let the game generate it, then load yours — but you when you switch objects, it will base the change off of the one that the game generated. It's a weird bug.