also,on my Onkyo 876,audyssey sets the center different from the mains and the L & R are set diff too,my center is sitting 30" higher then my mains and pointed a little down at an angle to the listening area,
and audyssey sets my left main higher than my R main(I assume from the different acoustics of my HT room),
what you are seeing is all normal,but like was said,you can check it with a RS meter,
I let audyssey do the basic setup then I go in and change many of the settings to what I like and what I think sounds good to my sources and listening preferences.
it's been said here that audyssey is just a starting point.