I have been using a Microsoft Sidewinder X4 gaming keyboard with ArmA 3 since Alpha release. Since then, I have been able to disable the start menu hotkey and use my left windows key as as a key binding in both ArmA 2:CO and ArmA 3 Alpha.
I am unaware whether this feature has been disabled on Bohemia titles across the board in an update, but now, I cannot bind left windows key to ANY Bohemia titles controls (ArmA 2: CO, Take On Helicopters and lastly, ArmA 3 BETA-both dev and non-dev)
Other games I own, recognise the left windows key as a binding perfectly, but unfortunately not in any Bohemia games. I have scoured the internet, performed registry edits to redirect the windows key as an available hotkey, executed scripts using "Autohotkey" and even just outright disable the key with no prevail. It seems it is a problem from the developers end, not the clients.