How do you have your computer connected to the Yamaha? Is it analog or digital? What listening mode are you using on the Yamaha? What kind of material are you listening to?

I know these are real basic questions but it would help me (us) to understand your set up. Those Yamaha receivers are pretty technical and have a lot of "unusual" options when it comes to setting them up. The more information we know, the easier it is for us to help.