Welcome aboard Allanroth,
Go into Options and to the control assignments - make sure you are on the cockpit controls and not a View Axis view...
Are you on v220.127.116.11? <- that is the latest.
Check the assignments to the Trigger 2nd position for the cannon, and to the Fire (?) button for the missiles. Maybe change them andsee what happens. You can always reset.
Reset may be a good idea, too. Here's a link - Majapahit's post in this thread