So I've noticed that the Saturn V pad at the KSC interferes with MLP's rotating service structure for the space shuttle. It looks like the hinge section collides with the launch pad, which I assume might be caused by your invisible spawn workaround? It's such a shame, considering how well the two play together otherwise!
Edit: On further experimentation, this seems to be an issue with the launchpad itself interacting with the part (not anything to do with your setup), I'll mention it to the Tundra Space Center folk.. Sorry for the scare lol