Speakers wired correctly?
I had this same problem in my WWF cabinet.
With the Sega NAOMI system there's usually a 2 channel sound amplifier board. That outputs (you guessed it!) 2 channel sound to the speakers.
So from the NAOMI system comes a standard red and white audio wire that goes into the sound amp board. out of that board come the speaker wires. There's a positive and a negative for the white and a pos and neg for the red. In my cabinet, some Yahoo twisted the positive and negative coming out of the white speaker connector - you know what I mean if you have this system - together (actually soldered them) and connected that to positive going to the speakers. Then did the same thing with the red positive and negative - soldered them together and connected them to the negative speaker wire.
I had to desolder them and I took the two negatives and tied them together and connected them to the negative speaker wire - same thing with the positive. Woohooo! Sound was great.
I also spent a HUGE amount of time swapping parts because it didn't even cross my mind that the cab would be wired wrong from the start. This was wrong throughout the machine's life! Check the wiring!