I gave you guys the benefit of the doubt and told myself that it was the room acoustics, but I tried it again and my co worker and I was just so impressed with the bass response of the A9.
When you say you "tried it again" - do you mean you listened to the speakers in the same location you had previously? If so, you have acquired no additional information to make any sort of judgment.
If you want to test for room response issues vs. amp issues vs. speaker issues, can you arrange to listen to both sets of speakers in the same room driven by YOUR receiver? With the information you now have, you can't differentiate between room vs. amp issues.
Unless something is defective with your receiver, it's not clear why there should be much difference between the two Onkyos. However, we KNOW room acoustics are simply HUGELY important for bass response. I have a pair of Wharfedale bookshelf speakers that shake the room they're in with their bass response. Of course, the room they're in is only somewhat larger than a walk-in closet, and they're getting all sorts of bass reinforcement from their positioning. They sound nothing like they did in their previous set up.
Regarding the source: what kind of format is your music in on your computer? Are you playing CDs and just funneling the output digitally to the receiver? Or are you talking mp3s, and at what bitrate? Or some other format?
ADDED BY EDIT: I looked through your posts, and see you're playing CDs, and sending a digital signal to your receiver (correct me if I'm wrong). In that case, room acoustics is far and away the leading contender.