It's a setting I believe, in case the trigger switch breaks. Check your menu. (Might be wrong on that)

Any luck? What setting?
I am having the exact same issue, this started happening after i re-wired the lights for the pop-bumpers, super-weird and annoying.

Make sure all flipper opto switches are engaging right in test. Clean the u shaped optos for good measure as well with windex on q tips. Intermittent issues could be just dirty.

Zero errors in test-mode though.
All of them checked and working except: The gun-handle trigger, i have not opened it up and checked, might there be an issue there?

Yeah, that's important to work as well. You'll have to pull it apart and clean it likely. It's been awhile since I've pulled one apart but it's like 4-6 bolts. Not too bad, theres a little push button in there that can get gummed up. Clean with ispopryl alochol until registering smooth, put back together and you should be in business.

I took it apart, the spring inside the mechanism looked a little messed up, adjusted that alittle bit, put it back together ( did not clean it thought, but will do ).
And now it worked perfectly now.. kind of weird since the gun-handle didnt contain any switch, there is just this little metal-rod touching a microswitch on the inside of the cabinet, but for some reason, the flippers does not fire the ball anymore.

I just had and solved this issue. The problem was the single drop-target bank. The switch that closes when drop target is down had lost its arm and cannot register, and also the diode. This causes the game to freak out when the ball is in shooterlane. This was in LX-5 ROM version.