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If your gamepad shuts off while in game you can't reconnect it. You have to log out of the game, close the client completely and turn it on before you can use it again. It's a real pain and I don't know if SE can fix it from their end, but it's worth a shot to talk about it.
Using a wireless 360 controller, by the way. I can keep it plugged in and charged, but the wires do get annoying after a while :\
Sorry if this was brought up before. Didn't look for posts about this.
Yeah this is very annoying for me as well.
I don't think this problem is related to the game. I'm using a PS3 controller and i run out of batteries often. I don't need to relog to reconnect my controller and I'm playing in fullscreen too. I think it's related to the drivers you are using.
Try using third party drivers instead of Microsoft's, if they actually exists for the Xbox controller.
I know that if i use the Xbox 360 emulator option in MotionInJoy for my controller, i get the problem you're talking about.
I tried googling to find some drivers but I was not so lucky. Maybe someone will post that uses 3rd party drivers for the controller.