I only just played with mine for the first time... got decent results, honestly. Kind of surprised me.
I don't know what you got going on in your scene, but what I would recommend to begin with:
Confirm your distances... don't change them, but be aware of what audyssey did. The distance is a delay adjustment so the sound waves from each speaker arrive at your ear at the same time. It is common as I understand it for the subwoofer to be set at a much greater distance from you than it is (because of DSP processing in the sub).
Confirm your speaker sizes and XO settings... you might need or want to readjust those.
Check your subwoofer sound... Audyssey set my subs HOT! Once I was done, I re-tuned them by ear. Upright bass in a small jazz setting shouldn't vibrate your @$$.
The Curve: First, I am not an acoustics expert, though I have had some schooling... so take this with a grain of salt, and remember, YMMV.
I knew I had an issue in my room being a little bright and lively... yet I have very neutral speakers. Sure enough, Audyssey took a chunk out right around 2KHz. Which was fine, but a little too much, so I lifted that dip a bit, not fully, and smoothed out the resulting curve changes with a slight bump to the bottom end. Nothing big, just a gentle increase in the lows, without extending anything. It is possible to do harm, as I understand. I just gave my bass from about 150Hz down maybe a 2dB boost, but brought it back to match the rolloff starting about -3dB at ~50-60Hz.
Then I listened with Audyssey, and switched out to Pure mode... and back and forth just to compare.
Biggest thing I can say, USE YOUR EARS. If you don't like it, scrap it and try again. If it is consistently making weird choices, you might need to explore other solutions.
To get some better help, you should post up info about your rig, room and listening dimensions, maybe a photo or two. The more info you give us, the better we might be able to help out!
Cheers
Oh, and don't forget that you have to send your app changes to the receiver. It does not happen automatically.