Sometimes during module development the menus created by the module can get mixed up, out of order, or duplicated. One is supposed to be able to fix this by clearing the menu cache and using the 'rebuild menus' function of the Devel module, but it does not always work.
The catch is that you usually can't delete menu items from the Navigation menu !
Even if you move such menu items you wish to delete to another menu, the delete operation will still not appear for those menu items ! The only solution/workaround I have found so far is to get into PhpMyAdmin (or another SQL client), search for the culprit menu items in the menu_links table, delete them, then use the Devel module rebuild function.
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