Key combination triggers second key on logitech extreme 3d pro

[Ironleaf 1]

When I played Arma 3 a couple of months back, I loved flying helicopters with my Logitech Extreme 3d pro. I had it set up so that I could control practically everything using key combinations. I used the buttons on the side of the joystick as "modifyers" such as ctrl or shift. Now when I came back to Arma 3, this seems to have changed. Now when I use my key combination for moving my head to the left, it happens, as well as looking to the left. Basically, the key combination works, but it doesn't override the original command assigned to the second button, and so both the key combination AND the second key itself triggers. Please help.