System icons puzzled me for a while, am not sure if I fully understand them even now but if you follow the code starting at " icons " you'll find adjusting and making persistent the additional /tmp/tce/xwbar.lst helped to control icons over a remaster. I use ezremaster and find that a persistent /tmp/tce/xwbar.lst works for my weekly remasters
You have to luv the wbar, it's classy but is also dynamic, so if you need the apps in a specific order then refer to freedesktop naming convention, which also controls the order of of items in desktop menus.