That URL syntax seems to only work with msysgit on Windows. I haven't found a form of the ssh:// URL specification which works on multiple platforms with command line git and includes more than one ":" character in the URL. Command line git tries to interpret the first word after the second colon as a network protocol, not as part of a path to the repository in all the Linux variants I tried. I suspect it interprets similarly on other Unix variants like FreeBSD, OpenBSD, Solaris, and HP-UX.
Note that it says "github.com:markewaite: Name or service not known".
It works if I perform the same clone but with "short notation" (no ssh:// scheme specifier at the start of the URL)
When I attempt the URL you listed in the bug report, I get a different error message than you get:
I ran tests on various git versions and various platforms using command line git and as far as I can tell, Windows (32 bit and 64 bit, Windows 7, Windows 8, and Windows Home Server 2011 running various versions of msysgit) is the only platform where the ssh://git@github.com:/github/git.git format works.
Debian (6, 7, and 8), Red Hat (6 and 7), and Ubuntu (14.04) all reject that format in all the versions to which I have access (32 bit and 64 bit). That matches with what you described of how you're using Windows 2008 R2 Standard.
It also tells me that support of that URL syntax is too platform specific to justify spending time fixing the bug for only one platform. It is a bug that the plugin rewrites the URL to an invalid syntax, but even if it didn't rewrite the URL, the syntax would be rejected by command line git on non-Windows platforms.
It is not clear what the problem is... the third slash?