I think you need to add "/api/v2/package" to the end of your package feed URL.
is the root url of the nuget server - the actual 'service endpoint' is probably at http://packagefeed.bluestonesolutions.l ... v2/package
NuGet.exe recognizes root urls and automatically appends "/api/v2/package" to the end and tries that. So, that is why nuget.exe is still working.
With rgpublish we took the decision not to automatically append the default service endpoint path to any root url specified because we can't always know that the path actually exists (it's not "/api/v2/package" on all Nuget feeds - like the embedded feed in Deployment Manager itself).
In the next month, we plan to add to the rgpublish commandline so you don't need to specify the root or path of the nuget feed at all. Instead, you'll simply be able to specify the name of the feed (that you have specified in DM) and rgpublish will contact your DM server to retrieve the feed's location and any API key.