I've found the solution for this.
Qubes is syncing all applications (more correctly all application shortcuts) from the following folder in the windows HVM:
C:\ProgramData\Microsoft\Windows\Start Menu\Programs
But not all applications shortcuts can be found here - some shortcuts like Internet Explorer, Notepad, CMD ... are located in the startmenu-folder of the user, which is located here:
C:\Users\<USERNAME>\AppData\Roaming\Microsoft\Windows\Start Menu\Programs
If some applications are missing in the Qubes "Add more Shortcuts ..." menu, you just need to copy the shortcuts from the user startmenu folder (c:\Users\...) to the general application folder (c:\ProgramData\...).
Then back in dom0 enter qvm-sync-appmenus YourWindowsHVMName and the new applications are available to be added.
If this info is not present in the qubes docu this should be added,for other newbies having same problem.
- P