I do have custom keybinds for helicopters but haven't used any game controllers. I'm using pure keyboard, not even the mouse.
My friends within the same server, running the same mods, and have played just as long as me have said they don't notice that big of a change that I'm talking about. I have also tried without mods. My friends have used keyboards, mice, and gaming controllers and have no issues. So I don't think it has to do with those.
Running Windows 8.1 64bit