I feel that the iconbox is another floating panel like the original panel, and most people (that use it) put the iconbox on the same edge of the screen as the panel. The iconbox should either mimic the "always on top" nature of the panel, or have its own setting to do so. It seems like a bug when you have them next to each other, both looking and somewhat acting like a panel, yet if you maximize a window to cover them, the panel is incapable of being behind the maximized window.
Ok, in the next pre-release both the panel and the icon box are always on top. The option has been removed.
Move bug to Window Buttons; the merge of tasklist and iconbox.