In most versions of Windows, a user can manually organize the order in which applications and application groups are displayed in the Start Menu. A user might, for example, drag a frequently-used application group to the top of the Start Menu and leave the remainder of the items in alphabetical order. The displayed order of items in the Start Menu is independent of the order in which %userprofile%\Start Menu is sorted in Windows Explorer.
Similarly, a user can manually rearrange items in the Favorites menu or Favorites Center of Internet Explorer (IE) independent of the displayed sort order of %userprofile%\Favorites.
These user-defined display settings are controlled by the Windows registry.