I've got a ST:TNG who's right side cannon doesn't recognize that it's been fired whenever a ball is shot from it. It shoots the ball just fine, and the test mode seems to see the opto sees the ball as gone, but the game play still allows the cannon to fire a second time with the game audio telling me to fire the cannon. (even though it's already been fired). If I grab the trigger and fire the cannon a second time ("Dry firing" it) game play seems normal.
Thoughts?