I wonder if anyone has
  1. Also noticed this problem
  2. Has a solution for my dilema

Apparently, something has changed wrt Github and it affects the ability to use Capistrano; specifically it affects the ability to CLONE repositories on a remote server.

I have written a Gist with details, but here is the 'gist' of my problem:

I am new to Capistrano and have one app that is working as expected. This was instantiated months ago and the repo in Github is private.
When I now try to setup ANY new instances (RoR projects) I encounter a problem. That is, during the "clone" operation in Capistrano (using agent_forward and SSH keys that work from my local machine) the "ERROR: Repository not found" error appears. But, as I have verified through testing, ONLY if I use a Github repository that is set to Private.
Furthermore, if I temporarily change the Public/Private status of any of my repositories I can get Capistrano to operate correctly.

I am not pointing to Capistrano as the cause of this problem. Based on the symptoms it appears to be something odd with Github (or git).
I would appreciate any insight. Post it here and/or on the Gist I created.