Change Configuration Manager restarts computer TO Configuration Manager controls restart AND support the Site Control List return codes
Currently, when a Program option is set to 'Configuration Manager restarts computer', the return code is evaluated for 0 or non-zero only. A return of 0 restarts the computer whereas a non-zero is considered a failure and does not reboot the computer. The Site Control List already has Success, SuccessRebootRequired and FailureNonRetry return codes defined. I'm guessing they are used for Applications but they should also be used for Programs.
Please change the 'After running' option from 'Configuration Manager restarts computer' to 'Configuration Manager controls restart' and support the Site Control List return codes.
** Maybe change Configuration Manager logs user off to support Site Control List return codes too :)