I think I've noticed this conflict between msys and the built-in OpenSSH and worked around it for years without understanding why it happens. Basically I find

I think I've noticed this conflict between msys and the built-in OpenSSH and worked around it for years without understanding why it happens. Basically I find that my ssh agent never works unless I set GIT_SSH to the builtin one (at C:\windows\system32\openssh\ssh.exe). Once I do that, everything is happy. If I don't, git over SSH doesn't work right. And that makes sense. When msysgit calls the Microsoft one explicitly, it uses the Microsoft version of the agent protocol.