After some looking around in Log files, I found that the icons that should be copying to All Users (Startup, Startmenu and desktop) profile are copying to C:\Windows\system32\config\SystemProfile (Startup, Startmenu and desktop). Why would it copy to a different location based on using the software deployment portal/policy rather than policy-supported push?
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After some more looking around in the MSI logs, I found that if a user is NOT logged into the computer, the MSI does a policy-supported push installation and sets ALLUSERS=1 and the icons all show up where they should. If the user IS logged in, then the ALLUSERS=1 property is omitted from the commandline, and all the icons are installed to C:\Windows\system32\config\SystemProfile.
If I put ALLUSERS=1 into the commandline when creating the package (under install/Uninstall options), then it is passed to the MSI and installs as it should to the All Users profile.
Has anyone else noticed this as an issue before? How have you worked around it?