Right, it's about time I asked for help.

[xhawaii808]

I have noticed that the shelf icon sticks and even though it has been removed, either by MMB dragging it into the trash, or by removing it with the Shelf Editor. It doesn’t go away until you force a redraw of the shelf by activating another shelf and then activating the custom shelf again.

If you’re really lost, you can always edit or delete the shelf_Custom.mel script. If you don’t know where to find that, the MEL command internalVar -userShelfDir; will tell you.