A lot depends on your room characteristics, speaker position, proper mic location when running setup, other noises in the house (needs to be dead quiet even after the chirps). Audyssey reports the -3dB point of each speaker in your room and reports that back to the receiver, which then sets all the settings (small/large, freq response, etc. ) If you have saved all the settings you never want to lower the crossover freq, ok to raise it, but lowering it will create a gap that won't get corrected.
You could try rerunning setup, look at your speaker positions in regards to toe-in, how close to wall, etc... Also make sure the mic is at close to ear level, and not on top of a couch/chair but use a stand or tripod. It can pick up reflections if to close to furniture.
Here is a nice video descibing some important things to think about.
http://www.youtube.com/watch?v=okyNlhJ3Hvo
