I had this problem on my new MBP 13. I opened up the case to figure out what the problem was....
Basically, there are a large number of collapsible bronze "pins" on the motherboard. Their purpose is to make contact with the bottom casing and absorb the shock of any impact so that it does not damage the motherboard.
For some reason, one of these pins in my machine was making a terrible clicking noise every time it collapsed (basically anytime i picked up the computer).
The solution I found was to stick a little soft adhesive piece of foam on the bottom aluminum plate, forcing the pin to stay collapsed. That solved the issue. You'll notice several pieces of similar foam like objects on the bottom case that perform the same function.
Are these pins viewable on the ifixit disassembly pics?