yeah, I think it's either 4 or 5 spots where the box can be. 1 is the room you start in, 2 or 3 of them are in the bottom, and then the second level, but it only moves there never starts there.
There is a way to kill the scientist too, it just takes a shit load of ammo. we kill him every time now, just have perfected the exact way to do it.