Thanks @GeoJosh. In my case, clearing usage reports with number-only names did not resolve the issue. We are running 11.1 on windows with two ArcGIS Servers participating in our site. I used server admin to delete two usage reports with number-only names. I restarted Monitor and both ArcGIS Servers. No change after waiting 2 hours, ArcGIS Monitor was unable to discover our ArcGIS Server site.
I decided to un-register the ArcGIS Server component and re-register it and it was immediately picked up. Is the work around you mentioned confirmed to work with a multi machine ArcGIS Server site?