Yeah, I agree with buckeye...if you're hearing differences with the frequency changes, then that sound like the sub is still on. You're sure you tried it with it set to off?
I have the 8400 and love it. There's a couple of ways to set it up to 2 channel. Actually, if you're just listening to a music cd, if you hit "auto" on your remote or with the jog shuttle, it should default to 2 channel since that's the signal it's receiving. There's also a selection for "stereo" (both on the remote and with the jog shuttle) which should do it. Messing with all of the other surround modes is just making the receiver take a 2 channel signal and "convert" it to various surround modes. Another way, and probably the quickest (if you're looking to run a quick check) is to click the button on the lower front side of the face (below the volume button) that says "source direct." This should bypass all bass management and will only play 2 channel signals. Keep in mind though, source direct also bypasses tone adjustment, so you can't adjust the bass and treble. Hope this helps.