Thanks for the reply.

I do already play in windowed mode, for the time being I use the plug-n-play adapter if I know I may be distracted but the one I have is defective and doesn't always work most the time. Guess I'll have to shell out a few dollars for the wired version of the controller. It just sparked my curiosity though why it can only resync at certain points of the game. Like you said, I'm hoping it's something that can be fixed in the new version! If not, not really a big deal.