Sounds like you either haven't saved the settings, or have done the setup more than once, so the auto has a different set of parameters than the saved configuration. I did the auto-setup, then played a CD, and wondered why it seemed lifeless - because the auto spiked the bass and treble curves to make them "flat" - zeroed it out, and BAM! Beautiful music... anyways, got real familiar with going back and forth finding how to "undo" what auto-setup had done, and the only time I saw what you did was having a stored setup, and an auto-setup that I cancelled...
Ive done the autosetup and didn't like the way it neutered the speakers - will try a re-run with it set to "Front" instead of flat...
Venger