I have the same issue, but using a razer Sabertooth controller.
Also tried with a Xbox one controller.
Adjusting sensitivity does not fix the issue however. (not even on the sabertooth)
Neither does disabling/enabling the device ingame.
They both work fine in all other games,
Also I have reinstalled all my drivers for them but that didnt fix the issue either.
Everything was working just fine before the latest update.
Since then, I can't fly using my controller any more, as the helicopters just dont respond correctly.
Out of all of this, I concluded this must be a issue within Arma 3.
Yours Sincerely,
Maurice.