A shot from the hip: process monitor log might provide further insight, hopefully we can see what the msi installer is doing. Bear in mind that the OS is doing all the work in this case, talking to the msi installer etc.
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Try re-ordering the path statement to start with c:\ Could be VSE is seeing the first entry as a UNC Share and stopping the install at that point. Or remove the %SMS_System_Path% entry and see what happens.
Figured it out. Turned out it wasn't a path variable that was hard-set in the registry. It was one that was being loaded into memory by a specific application when the app was first run. Hopefully, I will be able to sidestep this by performing the install after the end-user has logged off.
Thanks for everyone's input.