I hate to keep asking you questions like this, but welcome to remote troubleshooting... I see you have a Yamaha 2600. If you used auto-setup, I believe that model also does equalization on the speakers. Alan has mentioned (although people vehemently disagree with him) that he finds this to cause problems with the sound. There should be a way to turn off the parametric EQ and leave on the distance and level settings. Worth a shot, if you haven't tried it.

I am the Doctor, and THIS... is my SPOON!