After a clean install of windows 8.1, Steam and Arma3 i also had a problem with a disconnecting gamecontroller.
The gamecontroller is a Saitek Pro Gamer Command Unit.
I noticed that while messing around in the editor with VR scenes, there was no problem.
But the moment i started Altis the controller gets disconnected somewhere between immediately and some minutes.
That made me think about FPS. Turning off rotation blur and lower the overall visability settings in order to keep a steady FPS solved my problem.
If someone can confirm this solution?