During provisioning, the shortcuts might have created on the desktop and programs menu for the user (administrator) who installed the application. That might be the reason why it is not showing when assigning the AppStack to other users.
Two options:
1. Recapture AppStack and make sure to copy the shortcuts from Desktop/Programs menu to "C:\ProgramData\Microsoft\Windows\Start Menu\Programs". To show the shortcut on desktop of all users, copy the shortcuts to "C:\Users\Public\Desktop"
2. Instead of recapturing, go for 'Update' AppStack and do the same steps to create a new AppStack. Assign the new AppStack and check if the shortcut shows
