This happened to me back when I first got my 990, and long before the firmware update. I was playing around with BYPASS, switching my fronts between SMALL and LARGE and trying the various sub settings (sub, nosub, lfe-only). I found when I went from sub to nosub and back that my calibration level settings all were set back to 0 dB. I have not tried it after the update, and am not sure I want to.