Andrew Everard:
The Audyssey settings are pretty good as a starting point, but not infallible, and IME not as accurate as the stereo version of Sony's DCAC system, for example.
I have always tweaked by ear after running these auto-calibration systems, as I find they all tend to set the centre level a bit too low and run the surrounds too 'hot'.
If using an SPL meter I've always found the readings to be more accurate at higher levels - I usually aim for 75/80dB as a base level, and adjust other channels accordingly. Use the slow response if your meter has this option, and A-weighting if there's a choice between this and C.
I found this on my Denon's Audyssey setup. Ran the auto-setup and it was really off. I only have 3 real listening positions in my small room so I ran it again taking measurements at each position 2x and it was much better. But I was convinced the rears were too hot. Got out the SPL meter and sure enough the rears were 2 dB too hot and the centre was 1dB too soft. The speaker differences and the Room EQ were spot on though. My speakers have always been a bit over enthusiastic in the mid-bass and border on sounding artificial, but Audyssey picked this up straight away and rolled out the offending frequencies and now they sound much more natural and detailed.