First, have you mapped your controller for mode 2? If not, bring up the clipboard, click options, map controllers, check the auto select mode box, then in the drop down "mode selection" box select mode 2 (vehicles & gunners) then press copy mode 1 on the left side of the clipboard. This should give you a good starting point on your controller mapping for different modes.
Secondly, the gunner positions won't fire when you are on the ground, you have to be in the air.
Hope that helps.