I agree with Neil. I believe your icon cache is the underlying issue. Rebuilding the icon cache could help, but it's not a guarantee. You're probably better off fixing the icons with issues. Opening the Properties dialog and updating the icon, even if it's the same one, should help.
So, on your Start11 menu, right click an icon with the black background and select More>Open file location. Once there, right click the shortcut and select Properties. Click Change Icon and then Okay if the icon looks good.
For the few icons you have with black backgrounds, this will be much easier and faster than rebuilding the icon cache.