Check the ceramic capacitors at the switches under the playfield. Probably shorted. If so they can cause all kinds of havoc including not registering switches in gameplay but work in test mode. Remove them and see if the saucers wok in gameplay. Replace though, don't leave them out, because the system needs them to work properly. Its a 0.047 uf ceramic disk capacitor.

Check this out:
https://pinside.com/pinball/forum/topic/replacement-switch-capacitorolder-bally-pins

I misunderstood the original post and thought you meant they registered in test. It appears you meant the coils work in test though not the switches. My miss.

However bad caps can cause all kinds of issues. If you're going to be having old Bally games around then get you a bag of those caps. Even though all is working I'd go ahead and put one on the switch that is missing one.

dothedoo I stand corrected sir. My EBD had a cap on its saucer hole. I was having issues with phantom firings so went through replaced all my caps and there was one there. I never questioned it and replaced. Your comment made me chack my schematic and there wasn't one there originally and looking at the matrix above.... nope no cap on the saucers.Perhaps mine was a factory installed error or a later tech put one on? So disregard. No caps on the saucer switches. Glad you found your issue.