I have a dedicated MK2 cab and it has always exhibited this phenomenon. I have swapped other JAMMA boards into the cabinet and they don't do this. WEIRD. When playing the game at a reasonable or loud volume you don't really pay it much attention, but at lower volumes I hear it...like a hum or whine. When my screen changes during attract mode, it makes a little squelching sound as the screen changes from like the winning streak display to the next screen.
I thought maybe that one large capacitor on the sound board might be bad (possibly filtering the power supply?), and changed it out with a new one of the same value, but there was no difference. I also have another MK2 JAMMA board set I have tested to make sure it works properly, but I didn't think to see if it exhibits this "interference". I don't think either my MK1 T-Unit set or MK1 knock-off JAMMA boards had this problem.
I will try, if I can, tomorrow, to hook the other board set for MK2 up in the MK2 dedicated cab and see if I notice it doing the same thing. Would be nice to find out the cause once and for all, lol!