Sorry owenkhan, I just now saw your posts in this thread. I wish Pinside had a notification system when people post to threads...
Since you are not seeing the signal on the sound board J3, your should move back to the driver board to see if they are leaving the driver board correctly. You could go back and test PIA pins 10-16 to doublecheck.
The sound commands leave the driver board at J9 which is the bottom connector on the left edge of the driver board. Sound board signals are on J9 pins 1, 2, 3, 7 and 9 (pin 1 is on the bottom of J9 when installed in the game). These should be high through the pull up resistors on the sound board in attract (no sounds) and pulsing when in a game.
DO NOT TOUCH pins 4, 5, and 6 of J9 with your logic probe or you may damage it. Those pins have higher voltage solenoids attached that may damage your logic probe. You can try setting your probe to CMOS that may provide enough protection from an accidental connection. Some probes have input voltage protection in which case, you can disregard this warning.
If you have the signals on driver board J9 but not on sound board J3, you have a wiring/connector issue.
What is the state of the rest of your Firepower? Is it 100% working otherwise? Was the sound ever working or is this a new acquisition? Have you bullet-proofed your CPU/Driver boards (replace 40 pin, reflow/replace header pins, replace Scanbe sockets, etc)?