When you need to find out what element is being used for a certain location, Snoop is a great tool to use. Then once you find that you can look at the DefaultStyles directory and find the style for that element (or its ancestor). In this case that element is the PaneTabItem. The PaneTabItem uses one of 3 templates depending on where its being used. In this case its docked so its the one keyed by igDock:PaneTabItem.DockableTabItemTemplateKey. Looking at that template you can see that the background of the root panel has its background template bound to the Background property. Reviewing the PaneTabItem style, you can see that that Background is set to transparent - then there are control template triggers that would change the background to a particular brush. So you can probably just put a style for the PaneTabItem into the xamDockManager's Resources for the PaneTabItem and have a setter that sets the Background property to whatever brush you want to use - since the unpinned and documentcontenthost used PaneTabItems seem to have a background by default I don't think this should interfere with them.

Can you provide a screenshot that shows what area you are looking to affect? Note, we ship the default styles for the control in the DefaultStyles directory so you can use that as a reference for what brushes are being used where.