It was created as a package as per the Admin Guide and the package is set to run only when the user is logged in. I basically followed the Adobe Reader example from the guide. The Show-InstallationWelcome -CloseApps is part of the pre-installation step and it works great if I run locally on my computer with local admin rights.
For whatever reason the application we are installing has to be run as the user because it is profile specific, however, we do not provide our users local admin rights to their machines and the toolkit needs to be run with elevated permissions. If the SCCM package run mode is set to run as administrator, the package will not install correctly (again, because its profile specific). If the run mode is set to run as the user, it will fail because the user doesn't have admin rights to run PowerShell. So I pretty much think we are SOL and have a backup deployment that will work. The deployment toolkit just made it look more professional from a user perspective. Thanks for the reply!
For whatever reason the application we are installing has to be run as the user because it is profile specific, however, we do not provide our users local admin rights to their machines and the toolkit needs to be run with elevated permissions. If the SCCM package run mode is set to run as administrator, the package will not install correctly (again, because its profile specific). If the run mode is set to run as the user, it will fail because the user doesn't have admin rights to run PowerShell. So I pretty much think we are SOL and have a backup deployment that will work. The deployment toolkit just made it look more professional from a user perspective. Thanks for the reply!