The Deadworld mod DOES NOT cause the problems! It just is way more sensitive to problems that already existed. You have an opto problem either on the crane drop (or the crane isn't dropping it correctly), or in the trough. Very, very common problem on Judge Dredd (and other games of that era) and you can find many posts addressing fixing them with a quick search here or on RGP.
The cliff-notes (no pun intended there Cliffy!) version is clean all optos (alcohol on a q-tip works nicely), make sure optos all work, make sure crane drops ball consistantly through the drop optos, make sure your trough doesn't have divots (or even magnatization issues!) that can cause the balls to hang up, etc.
Since your game thinks you are only playing one ball when infact you have two on the playfield during/after multiball, that seems to be a clue that it's a trough issue. The game thinks one more ball is down there than there really is. I would start with the opto in the second to last position to the outhole (and the last one for good measure) and make sure it isn't blocked/dirty. If it were a ball drop off the crane issue, chances are your multiball would never end, instead of ending early. Of course anything can happen when you are chasing opto ghosts!
Best of luck! The mod is well worth the hassle it can take to get your machine up to speed. There is no cooler ball lock in my opinion!