Yes, unfortunately, the manuals were not written for us (home users), but rather casinos, who have a supply hotline to the manufacturer. The manufacturers (Bally, in this case) would much rather have the part replaced, for full value, than see anything "fixed" on a part, and the manuals reflect this.
If I had to guess, and don't pin me to this, but I would maybe start with your game limits, then look towards your chips (as they dictate the payout)? Just because the sticker on the glass says 40,000 doesnt mean the game limits were set the same. Not sure of course, but if it was hopper related, it would more than likely either NOT pay at all or just keep paying?