The closest I have seen to a problem like this was with a Sorcerer that was making the wrong sounds. It turned out to be bad ram in the sound section. I would also check the traces for the sound select inputs. However if you say the game makes the proper sounds in test mode, this may not be the issue.

In the schematics, there are 8 traces that run between U9 and U10 that are designated as ‘sound select’. Check the continuity of these traces. The these are used to pass the sound request from the main game computer to the sound section of the MPU. If one of these traces is shorted to ground or floating, it can cause the sound section to play the wrong sound.

Assuming your ROMs are good, the next thing I would do is replace the RAM in the sound section (U23).

Im glad to hear it worked out. It just goes to show you should always check prior work.