Did you use the FM-mod, or just a direct connect with your factory wiring?
IF you used the factory din plug, the first thing I would do, would be to disconnect the din plug in the trunk and inspect both connections. Any bent prongs or gunk inside. If no, then it could be at the connection of the radio, or yes one of the channels could have gone out in the audio pre-out section of the changer (not likely though).
BTW, I was under the impression that the proper changer for your deck (assuming it is the KE-91zbm) was the CDX-30.