After applying the Adapter for Microsoft Dynamics 365 And CRM 5.6.2 hotfix 14 to resolve the deprecation of Microsoft Dynamics 365 / CRM "Online" authentication. You may experience an additional pop-up window when trying to run jobs silently using the /RS command line switch if you use the "Tworkbench" command. This additional pop-up may cause an error for the "Tworkbench" command, visible in the Windows Event Viewer, and the job will not run.

To resolve this issue, update the command line or batch file to use the command "messageprocessor" instead of "Tworkbench." Although both of these commands will run the job, the "messageprocessor" command will honor the /RS command switch. The job will then run silently without any additional popup windows or errors. 

Further information on running a job from the command line or batch file can be found following the link below.

Running A Job From The Command Line or Batch File Help Guide