Controller Sending Double Inputs When Streaming

[Em]

I'm using Steam to stream a non-Steam game (the Gamecube emulator Dolphin to be specific). I have mapped my controller (wired Xbox 360 controller) successfully and the emulator is properly detecting it as an Xinput controller. The problem is that when streaming Dolphin, the controller will also send mouse and keyboard inputs. The analog sticks move the cursor, triggers click the mouse, and worst of all the B button is mapped the escape key, so I can't press it without exiting the emulator.

Is there any way to stop the controller from sending these keyboard inputs so I can use it properly?

[Enumex]

As far as I am concerned dolphin emulator does not like the steam overlay. My bro set up smash bro melee and well everything was distorted polygons were flying everywhere. When we turned of the steam overlay it went back to normal. However I am not sure that my problem is the same as your as only graphics were affected, and the operating system on the computer is linux.