Creating Prefab causes scripts to break, Copy/Paste Gameobject doesn't

Ok, this is a REALLY really weird question. I have a very complex GameObject that I'm trying to get from Scene1 to Scene2. The ideal solution would be to make a prefab out of it - which is what I'd like to do - but it doesn't work!

I drag it over to the Assets folder, it creates the prefab, and then I drag the prefab into the new scene. Doesn't work, the GameObject breaks and doesn't function like it should.

So, I take said GameObject from Scene1, right-click and copy it, mosy over to Scene2, right-click and paste it, and viola! The GameObject works exactly as it should be.

Is this a Unity bug, or is there something that I might have screwed up going from Scene to scene that might break it?!?

EDIT: So, I randomly tested it out. Deactivating and reactivating said GameObject (and it's script component) during run-time causes it to start working like it should??? I have no commands besides in Awake, so perhaps it's not being called correctly?