Orthanc, when it starts as a service, reads all the configuration files from C:\Program Files\Orthanc Server\Configuration which contains a worklists.json file that enables the plugin.
When you start it manually with your command line, you are actually providing it with a single orthanc.json configuration file and therefore, it does not get any configuration for the worklist plugin.
Here’s how you can start Orthanc exactly the same way as the Service does: "C:\Program Files\Orthanc Server\Orthanc.exe" "C:\Program Files\Orthanc Server\Configuration"
You should also, of course, always make sure that each Orthanc gets its own configuration for HttpPort, DicomPort and StorageDirectory hence you should very likely duplicate your configuration folder.