If you drag a launcher from the panel and drop it on the desktop, instead of ending up where dropped, as a icon dropped from within Nautilus would, it ends up in the default location after the last icon. This probably relates to recent changes to the drag-and-drop code ... I seem to remember it working before. (Testing with nautilus-1.0.4-29)
This is jrb's area of expertise ;-)
pass the buck.
Changing from an edged panel to any other type then back again also changes the placing of the icons.
The bug with icons being dropped was fixed in nautilus-1.0.4-33 or so. It's normal that the icons are moved to be within the rectangle enclosed by all panels - the idea is to avoid being covered by a panel; do you mean something other than this?