When logging onto the new machine I noticed that all of the installed applications had disappeared after a recent change to group policy. When unticking the Link Enabled option for the policy all of the programs came back. The group policy setting below was causing all apps to disappear except the application which was installed in the users profile.
The help text assocated with the setting:
Removes items in the All Users profile from the Programs menu on the Start menu.
By default, the Programs menu contains items from the All Users profile and items from the user’s profile. If you enable this setting, only items in the user’s profile appear in the Programs menu.
Tip: To see the Program menu items in the All Users profile, on the system drive, go to ProgramData\Microsoft\Windows\Start Menu\Programs.