What volume settings and crystalizer settings are you running?
On mine, if I turned the volume in the control panel to 75% I could hear noticable signal degredation. My remed for this was to turn down the volume there and then turn up the physical volume (this on the front panel and listening through headphones, so this would be the volume on the Z-5500s control panel). I turned it to 50% and it got rid of it at any volume I listened to (turned it up pretty loud to check).
You might play around with different settings. Check and see if you have CMSS, EAX, or any other settings turned on that might be causing it as well (I turned off all of them, including the Crystalizer).