deploying a bath file with SCCM
copy "C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Cisco Jabber\Cisco Jabber.lnk" "%USERPROFILE%\Start Menu\Programs\Startup"
You need the SCCM 'Application' to run as the User and not as the SYSTEM. This will allow the batch access to the users profile.
I dont have my lab up so I cant show you the dialog sorry. I cant remember if its during the creation of the SCCM application or during deployment, when the option shows up.