This seems quite odd, when I think of this.. I tend to think of it through the following analogy...
If you take the hard drive (the brain in this example) of your computer in it's current state, properly install it on another computer with different specifications (different motherboard, video card, etc.), there would be a lot of confusion with the "brain" (the hard drive in this case) of the computer.
If a brain transplant were theoretically possible, that is to implant a brain into another body, wouldn't the brain simply malfunction because it is now controlling the processes of a body it is completely unfamiliar with?
Now I know it is very very very unlikely for brain transplants to ever occur, it's sorta entertaining/intriguing to simply think about it. 🙂