This should be controled by alt-1 and alt-2 as Gizmo stated. If you change the background color of alt-1 or alt-2 you'll see that it will change the shoutbox colors on the main page.
There is actually a bug here in that it really should be set by left/right-alt-1 or 2 but it's not working properly. Right now they are just falling back to alt-1 and alt-2. I think you need to get rid of the background color in the link properties. By default the background color of linked text should always default to the same color of the background itself.
