Installation of the VDA through SCCM fails on a few machines

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To override the default, specify the noresume parameter in the installation command. This prevents the VDA from creating this registry key and run the installer a second time using a second task sequence to finish the install Task sequence with SCCM:

1. Install VDA: XenDesktopVDASetup.exe /noreboot /quiet /components VDA /noresume 
2. If you see Exit code 3 in the installer logs, reboot the machine
2. Run the same command a second-time VDA: XenDesktopVDASetup.exe /noreboot /quiet /components VDA /noresume Exit code 0 Reboot

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Problem Cause

An installation of a VDA is divided into two main parts:
1. Installation of the prerequisites
2. Installation of the VDA

The installer automatically installs and enables Remote Desktop Services role services, if they are not already installed and enabled. The installer automatically deploys the following requirements:
• Microsoft .NET Framework
• Microsoft Visual C++ Runtimes, 32 and 64 bit

This is also documented in https://docs.citrix.com/en-us/citrix-virtual-apps-desktops/1912-ltsr/install-configure/install-command.html “By default when a machine restart is needed during an installation, the installer resumes automatically after the restart completes.”

By design, “Run and RunOnce keys are run each time a new user logs in.” this must be an interactive logon i.e. this will not be triggered by the system account https://msdn.microsoft.com/en-us/library/windows/desktop/aa376977(v=vs.85).aspx.This can cause an issue if the SCCM sequence is run as a "system" as this resume of the installer will not be triggered on reboot. You will also leave behind a run once key which will then be run on the next "user(interactive)" logon.