Did you delete any icons in the Bundled Images category? Otherwise, what version are you using? Free or Plus? OS? Service Pack? Do you have the latest update?
So did you delete any icons in the Bundled Images category from the ObjectDock installation folder? If you did, it might replace them with blank icons. Try clicking on the empty space to see if anything happens. If not, contact Stardock Support.
I'm having a similar problem with certain icons. They just go invisible randomly. Exiting Stardock fixes the problem but eventually it happens again, one of the icons just go invisible. This just happens on the SD taskbar.