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 🙂