I've been having a problem with my 32X where the normal audio seems to be perfectly fine, but the PWM audio generated by the 32X only comes out of the right channel. I've tried cleaning/reseating the ribbon cables in the 32X and cleaning the edge connector that goes into the Genesis, but I haven't had any luck. This is with a model 1 Genesis (I'm using the headphone jack plugged into a Sega CD's mixing port for output, if that makes any difference).
Have you tried narrowing down the problem to see if the issue is between the 32X and Genesis or between the Genesis and Sega CD? . Use some regular headphones to see if you get the audio correctly prior to send it to the Sega CD.
I listened to it through the headphone jack and it sounds the same- PWM only on the right channel. Come to think of it, is the PWM audio on the 32X dual mono or actual stereo? If it's mono I might see if connecting the two audio pins on the 32X's edge connector (B1 and B3 IIRC) will fix the problem.
I could swear it is stereo (B1 & B3 separately ) but don't quote me on that. Although when I did the 32X compatibility mod to a Genesis 3 I ran into a similar problem.