This was found to be a bug with the web adaptor and the way ArcGIS Explorer initiates the request to add a server. ArcGIS Explorer sends the request using a slash, '/', after tokens in the URL. This is a known bug with the web adaptor, [#NIM082930 ArcGIS Web Adaptor (IIS) needs to handle redirect when tokens are accessed. ].
The request should still work with the slash regardless, and that is why the bug was logged. The web adaptor is fixed in version 10.1 service pack 1 allowing the request to be made with or without the slash so ArcGIS Explorer can add the server connection.
Service pack 1 is due out this month. See "ArcGIS 10.1 Service Pack 1 Announcement", http://support.esri.com/en/downloads/patches-servicepacks/view/productid/160/metaid/1898.
Thank you for contacting Esri support. This incident will now be closed.