This issue comes up from time to time. Two of my machines had the issue. The symptom is that my custom sound board will not play many or any stock sounds. It will mostly only play the background and solenoid sounds. At the end of the game, the background will continue to play. On the other hand, your stock sound board appears to play fine.
When this occurs, it is very likely the S4 (Address E) command line is floating. This is the 5th command line to the sound board that is only used by the sound board. My board cannot detect stock sounds, but the stock sound board will be off a bit (playing too high of notes).
The S4 command line is on the MPU connector J1 pin 7. It is on the sound board at J1 pin 12. The problem is likely at the MPU connector. Reseat, wiggle, and ultimately repin that connector.
In this video I show what my board does when S4 is floating. Then I show the stock sound board and how it sounds different when the S4 is connected.
