I hope I'm not jacking your thread, but I have the same issues with the ARMA series. I've tried completely wiping the controls and mapping only what I want to my wired Microsoft Xbox 360 controller, and still have issues. Analog controls, multi tapping, i.e. "key/button x2", or using 2 together i.e. "button + button".
I've even tried Xpadder, and just about every other tool out there. No matter how much time I spend or how many times I start over from scratch, there's always an issue with certain things, especially analog controls. Perhaps there is a way to directly edit the default control setup listed as "controller with scheme" through notepad or something? At least for the people who don't mind going the extra mile or seven, but just want it to work?
I think a little more support/ease of use, especially for popular controllers would open up the game to a much wider audience.