Chris: If you post over at MAMETesters.org it's likely Derrick Renaud (the discrete audio guru) would see it. Be warned: the current pitch is set according to Atari's schematics, and you are attempting to prove that Atari misprinted them. That's not actually uncommon - the Pong schematics have multiple errors - but it's still sort of a tough thing. (A picture of the relevant resistors/capacitors from a working PCB would suffice).
ETA: Also it's possible (actually likely given how often Brad updates it) MacMAME doesn't have the latest fixes. Try it on 100u2 on a PC for best verification.
ETA2: It's possible the pitch is controlled by a variable resistor on the board. In that case, press ~ and adjust the various discrete component values until you get the correct sound and report those values @ MAMETesters.