Hi,
Having similar issue since Yesterday.
I've W8.1, and an Xbox 360 controller working perfectly on any other game.
When launching game and without going in game, controller is there in the available controller.
When playing in the editor Ive no issue
When starting multiplayer game, controller is present at the beginning, but disappear after a while.
Ive deleted ARMA and ADDON/MOD and reinstall -> same issue
Ive reconfigured all the key starting from 0 -> same issue
Ive Throw the gamepad through the windows -> broke the gamepad...
Bought an XBOX one controller and redo the same -> same issue
Help will be greatly appreciated :)