Are you using ASIO or DirectSound? Also, XP or Vista? Regardless, I would check your Sound settings in both Windows and MC. In Window's it's Control Panel --> Sound... Look at the device properties for whatever you're using. It's possible the output setting (e.g. CD Quality, DVD Quality, Studio Quality up to 192000KHz) is not the best match for your setup.
I used to have J River set up to use ASIO on my Logitech Z Cinema speakers (via ASIO4ALL, since the speaker's USB connection doesn't natively support ASIO), and I would notice that poorly produced files would either give me an error about the KHz rating being incompatible OR only play on one channel.
Chances are the files playing on the left side are mono (not stereo) and your Windows/MC settings are more fine-tuned than the other media players, which I've found typically just spit out the mono channel in both left or right. Which would mean that MC is actually giving you the more accurate (if not unpleasant) sound.