It ain't 12km tall! It's the stability towers, they start flashing around the rocket like they are still attached, even after being left stages behind and back attached to the ground. It seems to be when the parts they were attached to reach the ground and explode, they get reattached to the ship. I think I just need to rebuild the lower stages with the new version, after re-attaching just the SRBs, it got better, they still glitched in while my lower fuel tank was attached, but they seem to go away when I separate that entire section.