I have mine apart right now as I'm converting it to WMS/Bally flipper mechs (waiting for a couple of parts), but it will be back together this week. If I recall correctly when the moon drops the ball a ball from the trough is immediately launched and the VUK replaces it after it runs through the subway.
Check the outhole trough -- it's pretty common for a ball to hang up and not run all the way down (e.g. you have an indication of balls 1-2-3-5 -- instead of 1-2-3-4) and if that's the case the game will not throw the new ball until it figures out what is going on (if the "missing" ball is missing long enough it will complain and throw a tech advisory as well.) There are two causes of this -- one is balls that have gotten too magnetized and stick together, but the other cause is the trough switches -- unlike Williams games which tend to use optos they're physical switches and if a ball is in there just right and the switch a bit sticky it can hang up. If that happens you should be able to see it in the trough looking down the outhole; when the VUK fires and tosses the captured ball in it would run the stuck one down the trough, the game "finds" it, and clears the fault.