While we'd all like to believe that Audyssey's automatic calibration and EQ is an audio panacea, it isn't, and it's error prone. I suggest you use your Radio Shack Sound Pressure Meter and adjust the levels and distances manually. You can tweak the levels of your surround speakers, subwoofer and center channel by ear if necessary later on.
Leave Audyssey Equalization switched off. As you've discovered, with really linear speakers like Axioms, Audyssey may degrade sound quality.
Incidentally, it is pink noise (not white noise) that is used. Pink noise has equal energy per musical octave; white noise has equal energy per frequency, so it's heavily biased towards the upper midrange and high frequencies.
Axiom Resident Expert