Are you using some named common configuration of litestep and various modules?
In other words, if you name the theme your using someone may be able to help you ;) (Better saying: "This theme has trouble" rather than: "It has trouble")

2. This might have something to do with that iTunes trouble, or is it different? (Just the icons?)

3. They dont go away? Are you "deleting" the actual items, or "removing" them from xDesktop config? (Or even worse r u using some different icon module?)

More people can help the more info you give us ;)
OS
Installer
Core version
Theme
Modules used
etc