WB By nature changes the System/Windows Color settings with each skin applied. So yes WB would still recolor any unskinned items, as it can not remove System wide color settings to that specific application. As you change from skin to skin WB will change the system wide color settings to match those specified in the skins settings.
How ever in tools/options/content/colors,In FF settings. You may be able to override Color usage by FF. I havent messed around in there lately, so I do not remember the full scope of the color settings that can be adjusted. But it may be worth a shot...
Hope this helps...