Only thing I can think of might be Move It, since some lights glitch out after a reload when they have been moved with Move It. Never seen it on a building though. :S
Interesting! Sounds like a bug in Prop It Up. It's worth keeping an eye on Prop Switcher. Right now tree swapping is disabled until a bug is fixed, but once that's back in, I would try switching to it. Hopefully it wouldn't have those bugs.