The most likely reason is poor setup technique. Audyssey can be 'fussy' to get the best out of it.
I suggest reading the FAQ, or the 101 or the Setup Guide linked in my sig and then coming back for more help if you can tell us you followed all the correct procedures very carefully.
The 'highness" of the "end" of the speakers isn't an issue - Audyssey could care less what speakers you use.
What do you mean by "overcompensating in the upper range"? Too much or too little treble?
I will definitely read/follow the links in your signature and report back.
Overcompensating means too much treble. Speakers start sounding almost harsh.