This is an issue I ran into when testing for this:
Might be worth a look?
We have what we call an invoke script which is called by SCCM, that identifies what kind of session is logged in and then calls “Deploy-Application.exe Install / Uninstall” we have 3 different ways depending on what it finds. We have even gone a little fancy and integrated it back into “Deploy-Application.ps1” so we have less scripts to keep up-to-date!