Have a read through the Judge Dredd club thread, this issue has been covered many times. It's most likely going to be an opto problem somewhere, possibly the trough and could also be the crane drop opto as well. To test the trough opto's, remove all 6 balls from the trough, go into switch test and then roll the balls 1 by 1 back past the flippers into the trough. If all opto's are working it will register them all as the first ball rolls into the trough to the end. That's a good start, if the trough opto's are all working then start testing all the others, ramps, crane drop, etc. The crane drop opto, when not working well, in particular can make the machine do some weird things, very much like you have described

Super game starts with 2 balls until you knock down the Judge targets, then it's 6. If the music that plays when multiball is normally active is still playing with only 1 ball left on the PF (a good indicator) then the machine still thinks there are, at the minimum, still 2 balls in play. This is most definitely an opto related problem, i've had the same issue in the past and so have many others in the JD club thread.

Where is the 6th ball? There should be 6 in the trough unless you have 1 in orbit on the ring.

https://www.johns-arcade.com/product-page/trough-opto-board-7-optos

These one's? the Homepin replacements are very good, far better than the originals.