Only the map image files are showing up in Portal. When you share from Server to ArcGIS online the feature layers show up, not so with Portal. Is this just the way it is?
Sharing from desktop works when you are signed in. We like to share from server because if you forget to sign in while publishing in desktop you miss your chance to share to portal, if you overwrite existing service the "sharing" functionality does not show up and you need to share via server or delete and re-publish the service when signed in.