There seems to be a problem using Bluetooth controllers where it will intermittently stop working and start working again.
I'm using the Xbox wireless controller with new batteries and I tested other games and this doesn't happen. Sorry if this isn't the right venue but please check into this.
Update: after doing some research it seems that when using the Nvidia graphics processor it can cause some sort of a resource issue. I choose to use the Intel processor through the graphics setting in windows and now the controller works no problems as of yet. Hopefully this issue can still be resolved as I would rather use my Nvidia graphics processor.