I have never encountered a situation where the plugins are successfully registered and do not appear on the plugins endpoint. Are you certain you do not have two Orthanc instances running ?
If you have installed Orthanc using the official installers, then Orthanc is already running as a Windows service in the background, with all the plugins enabled. This is for instance explained in the (very old) Beginners’s Guide to Orthanc by Emsy Chan - By the way, it would be nice if some contributor could create an updated version of such a guide for Microsoft Windows.
I would strongly advise you to remove all your current Orthanc installation, then start with a fresh install.