I had until changed out the opto boards. I am not 100% sure the board was the problem. Maybe the beam was bouncing off the balls a registering the wrong receptor. I don't know. Something about that trough is black magic.

Remove the opto boards, clean the optos with windex and a qtip.

Inspect the boards for cold solider joints. Reflow the solider pads on the board connector pins, and also the optos solider points on the back of the board. You should never have the error again after that.

Sorry, EDIT I just read you had new opto boards. Clean all the other optos in the game with a qtip. If any have dirt or grime on them they will mess up the whole opto switch matrix. Common for JD.

About filing the holes, not sure if that was a good idea. But start by cleaning every single one. Even in the habitral multi layer ramp. Ramps. Deadworld. Crane. Under the deadworld etc. ALL OF THEM! Even look for any hidden ones.
Inspect those for cracked pads on the opto solider points too if you can see them withou removing a ton of stuff.

But definately start by cleaning them.
Probably 100% the problem.

I had the same exact issue and had the glm boards. There actually was I bad connection on the board at the plug so I ordered another board and has been fine since.in test mode wiggle the plug on the reciever board and see if any switches go off . Mine was a new board to but had a issue with it ,number 86 also must be a bad batch of boards or something .im sending it back to tony to get fixed , at least ill have a extra one lol.