You cant really explain it without knowing all the different gear and sources as you say. And without knowing his buddys sources. And you would think he must notice this on all his music, not just the specific CD which makes it more obvious. Because if it was just a certain cd or song, I think or hope he would have the smarts to know that it was that particular track or tracks. However he did say while in the motel room and listening to it through a Bose setup, he did not hear it. While the issue could be a number of things, the odds are it's a good bet that it's due to the gear not matching up and playing nicely together. If you don't properly match up equipment, sorry to say but these things are going to happen. Sorry to say but that AVR is not going to like driving a 4 ohm load, let alone when it is dipping down to below 3 ohms.
There is also the possibility, it's not the gear at all. But an incoming electrical issue. But he did not say he noticed the problem before the new gear. Sounds like all was ok with his old Onkyo unit and Klipsch speakers being used together. Which tends one to believe the issue would seem to boil down to his new Denon unit. Either way i'm just throwing out possibilities to help trouble shoot. I along with many others im sure ran into some of these same issues when first getting into the hobby. But with time, troubleshooting, knowledge and matching up gear properly, these things are less likely to happen.
Throwing all the possibilities out there is the best way for him to trouble shoot and figure out his issue.