I have solved this problem.
Go in and associate everything in your drive to have the "Authenticated Users" group. Do this by re-adding "Authenticated Users" group back into all file and folder profiles.
Aparently for an unknown reason, when I moved some files from another drive used with yet another version of windows this group went away.
This will resolve the missing programs and if you also want "Administrative Tools" to show up you will need to enable it in the start menu settings under the "Customize" tab.
Easy thing to fix but hard as hell to find the answer