My machine did same thing and i had a bad wiring connection at the ball trough opto board. If you look at them when the machine is turned on wiggle the harness and see if the status lights go out. Mine did and all I had to do was repair connector wiring. Or you can do switch test and see what is missing ball wise in trough or in the other optos that hold balls under playfield on left side of machine in the middle.

So be sure to check the divertors in the subway to see if the coils are firing. It sounds like maybe the one that diverts a ball to the right side of the subway isn't working properly. If the coil isn't firing during coil test, be sure to check to see if the tieback mod has been done.
http://www.pinwiki.com/wiki/index.php?title=Star_Trek:_The_Next_Generation

Correct, this is not crazy and will absolutely happen if your diverter isn't working. Fix the root cause of that and you'll almost certainly fix your staging / ball cycling problem. Personally I'd start with the simple stuff and make sure it's not just a broken wire at the diverter coil

Most likely the tie back wire has broken off, and a transistor on the secondary board has fried, which toasted the coil. Extremely common.

Here is a good tread about modding the connection, and links to more info on it.

https://pinside.com/pinball/forum/topic/sttng-tieback

Could also be as simple as the diverters themselves have never been cleaned and the original grease has dried and hardened preventing them from working.

Both posts #8 and #9 have happened to me at different times. The first was the divertor grease seizing up. Then later the tieback problem arose as I didn't find that the tieback was ever done correctly. Fried a component on the auxilliary driver board which I had to send out for repairs. So check to see if the tieback was ever done and do that for sure. And check the divertors and make sure they move easily and freely.