Ya so I think I figured out the problem. It wasn't apex that did that, it was GWX+windows. What happened was for some people windows apparently tried (and succeed in many cases) to forcibly install Win 10. The way windows did this was to quietly make the win 10 update a 'recommended update' and then switch windows update to automatic updates. A pile of people and companies got nailed with this little bit of bastardly behaviour. No one is sure exactly how they did this, even a number of IT professionals also got hit with it.
So your rather lucky you caught it and didn't end up with win 10. The fact you were running Arma APEX had nothing to do with it, just a coincidence (a problem with empiricism

).
It really couldn't have been ArmA. To do what your proposing it would have to act like a virus. About the worst Steam could do is install MS redistributables. Now the official MS redistributables would have the ability to change settings, and its possible the problem originated from them.
Anyhow neither Dowly nor myself could find the slightest evidence on the internet, that anyone else had your problem with ARMA.
Also as for windows 10, your safe now as MicroStupid isn't offering it for free, or forcing it on peoples machines.