Controller connecting problem with new skin.

I just recently bought a new skin for my xbox 360 controller and took apart my old controller to put the new one on. When I tried to connect it wirelessly and the light on the controller would flash but not connect. The only way to get it to connect wirelessly I had to take the battery pack out of the controller, connect the controller to the console with the cord and then put the battery pack back in the controller with the cord still attached then take the cord off. but I had to do that every time. I need some help to figure out what is wrong.