While using nestopia sometime with online play only i'm having issues with my controller. I've tried using a ps3 (with motionjoy), xbox1 and a generic windows controller and all have this issue. I always reconfigure the controller and play offline and it works, then when I connect to netplay and try to play it most of the time will not work. If I restart nestopia a few times it will work. When I play with my friend it will happen to both of us (not necessarily at the same time), so its not just my pc.
Any ideas on what is causing this or is this a common problem. Thanks in advance!