This is purely a guess, but if you get noise when you are scrolling through menus, it is quite possible that there is some interference/noise being generated on your motherboard which is affecting your onboard audio chipset.
It is unusual to experience it over a digital connection however.
I used to have terrible trouble with noise during scrolling etc from my onboard realtek chipset on my gaming PC, so I ended up buying an X-Fi Gamer card and the audio is now crystal clear. I prob wouldn't recommend splashing out on an X-Fi card for a Media Centre (I have my own audio problems on my Media PC which I am still working through) but you can get a PCI card that should work for about $50 eg a Aopen AO63060
COBRA AW-870LP 7.1 and use the drivers developed at
http://code.google.com/p/cmediadrivers/
Again, just a hypothesis.