Common troubleshooting steps to replicate how ConfigMgr operates prior to testing out deployments is to determine how an applications reacts when running as System.

A useful chink in the armoury here is to use PSTools from the SysInternals Suite.

Launch PSExec from a command prompt and run the following:

psexec -i -s cmd.exe

Hey presto a new window operating as SYSTEM 🙂