First check which list you are using by opening Classic Start Menu settings ->
Main Menu tab - whether it's the
Recent list or
Frequent list. The Frequent list should not show shortcuts which are pinned to the Taskbar.
• To permanently hide a program from the Classic Start Menu's Frequent list, use this "
NoStartPage" method:
http://support.microsoft.com/kb/284198.
• Some programs won't hide with "NoStartPage" method (some new desktop app shortcuts use AppUserModelIDs). To permanently hide these or Modern app shortcuts from the Frequent list, use this method:
http://msdn.microsoft.com/en-us/library/windows/desktop/dd378459(v=vs.85).aspx If you need help hiding a program that uses AppUserModelIDs, feel free to ask here if the MSDN documentation is too complex and I will elaborate.
The data for the Frequently used programs list is managed by Windows and it is encoded in the Registry. Its format has changed from Windows XP so editing with third party programs to edit the Run count is unsupported and may not work at all. The Frequent list is an automatically populated list. Above it is the
Pinned area where you are supposed to put any shortcuts that you know you use frequently and reorder them as you want. Pinned shortcuts are static so their position will always be fixed.