Yup ball trough issues.... flakey opto / cold solder joint or even wire lose in the molex connectors

I start with changing all the transmitter optos on the transmitter trough opto board. That is where majority of the issues start on this game.

Yes, had this a couple of times as well. Couldn't figure out where it was coming from, I never had (obvious) ball through errors. Maybe the occasional ball count errors because I whacked one out of the planet though...

I'm running on the deadworld mod rom, so that's like version L-0.1 or something. Really want a deadworld mod rom that has been fully updated.

I've had this happen a couple of times, I believe that depending on the settings, every now and then it will throw a random multi ball
that will seem like it never stops. I get the same thing on my STTNG, it will throw you a random ball, I think just to F-- u up.

My JD has a similar issue. Every once in a while a normal multiball will spit unlimited balls until the 4 judges have been destroyed and the ultimate challenge starts and then the game will go back to playing normally. I discounted it being a trough issue because of how reliable it goes back to normal. I am thinking it may be a dead world mod issue. Yours may be the same bug/glitch?

No. Mine has the dead world mod andhas no random failures

From Pinbits website.

Troubleshooting Notes
The locking software is very sensitive to hardware errors in the game. A few typical malfunctions and their fixes are as follows:

Diverter does not load the ring when planet lock is available
- Check ramp entrance opto
- Check diverter

Multiball does not have all 6 balls
- Insufficient balls in the machine
- Trough divots holding up the balls (gently file and sand the trough ball lane to remove them)
- Bad opto transmitters or receivers in the trough (check trough optos in swicth test)

Game keeps shooting extra balls in multiball, and ends ball with balls still on the playfield
- Check crane exit opto
- Check that the ball exits through the crane exit opto

The crane opto has a relatively long gap; cleaning the transmitter and receiver can help.

https://www.pinbits.com/index.php?main_page=product_info&cPath=13_8&products_id=136&zenid=b9c7f3f72472708939fa35ed69d9d1c2

MY JD did a multi ball on the second ball, and never lost track of balls, ran for what felt like 3 minutes straight.
I have the dead world mod. Don't think its a error, just random multi ball.

My JD also experiences this exact issue as described by the OP.
Running L1AT with Deaworld Mod.

The plug you need is available from many places - I have linked the parts required all available from GPE below.

I would be happy to post you a plug but it would probably take over a month to arrive.

5 pin housing:
https://www.greatplainselectronics.com/proddetail.asp?prod=CP100-05-LR

Pins (4 x reqd):
https://www.greatplainselectronics.com/proddetail.asp?prod=08-52-0123

Polarising pin (not really needed but nice):
https://www.greatplainselectronics.com/proddetail.asp?prod=15-04-9209

I had the same issues woth demolition man and it was wires going to the trough.

I tested it with getting into.switch levels and knocking on various parts of the pf where vibration could kick the optos into.flickering on the levels test.

I think you are having the same thing