I found I needed to define the DESKTOPDIR, and MYDOCUMENTS variables in the command line when installing silently with SCCM.
It seems the installer references something that doesn't exist within a system account context, therefore needs to be defined manually.
The below command is tested and working with ZebraDesigner 2 using SCCM.
"Zebra Designer.exe" DESKTOPDIR=C:\Users\Public\Desktop MYDOCUMENTS=C:\Users\Public\Documents ALLUSERS=TRUE /s
I also found you could extract an MSI from the original .exe, but it doesn't install silently, even with the definitions mentioned above.
Setup Type: Windows Installer (Delivered as an EXE)
Deployment Method Used: Vendor Provided Command Line (switch driven)