I was using ONKYO 905 which uses Audysee. I use the auto-setup feature. I measured the room responses with Audysee EQ on and off and I found the Audysee one has more spikes in the high frequency portion. I did some listening tests and found the sound was a bit harsh with the audysee on.

I doubt if the omni microphone that comes with the ONKYO has poor high frequency reponse which results in adding more dBs in the high frequency portion.

Has anyone notice the same problem as mine?

M

Some have but that was usually attributed to some slip-up in the setup. I suggest you consult the 'official Audyssey' thread and, in particular, an evolving document summarizing the tricks and insights related to setup.