Having the same problem with the XBOX360 wired Controller and with my Saitek (Mad Catz) F.L.Y. 5 Joystick. I'am using Win 8.1 64bit.
After starting ArmA3 i see both in the configuration at the main menu. When I join Multiplayer both disappear after a while. I don't have the problems in the editor.
I think i have this problem since a few weeks or months. Can't say the exact date, I was playing other games for a while. It works well before.
best regards,
predaiien
(sry for my bad english :) )