Graham, you are exactly right. The next step in my setup is to open up the plywood backing by drilling a large number of holes of say 50mm diameter (2"). The other alternative is to add an absorptive lining to the flat faces of the stand. Either way this will reduce reflections. This is made even more important by the fact that the Logitech satellites put out a fair bit of sound through the ports at the back. This sound is very 'peaky' at 2kHz.
Scott, I made a decision to only carpet the four main areas as I didnt need to cover the relatively small available areas on the front and back. So far this has worked well. I believe if someone took a little more time they could extend the carpet to cover these areas. My eventual goal will be to protect the heatsink during transportation with some kind of cover.