The article [Q177482] explains that shortcuts and folders may not be in alphabetical order and that new shortcuts created may be added to the bottom of the menu which occurs when you have manually rearranged shortcuts and folders on either the Start or on the Favorites menu, or when you installed a new program.
Note: This manual manipulation causes Windows to add an "Order" key in the system registry that you must remove in order to revert to the default sort process (alphabetical) -- any folder which you have personally manipulated previously will have this "Order" key added. Simply follow the instructions in this article to find and delete each "Order" key found.
Whenever I add a site to my Favorites list (IE 5.5) it is placed at or near the very bottom of my list. This isn't a problem but when I manually move the new listing to its proper alphabetical place in the list it won't stay put and appears back at the bottom of the list the next time I open Favorites. Any thoughts on what is going on or if I'm doing something wrong?