I figured it out, I have Cygwin installed and I put it in my path environment variable. Turns out the git installation from Cygwin was interfering with the regular up to date, git installation. This was causing go with args to only work if I had the Cygwin terminal running. On golang-nuts someone also mentioned that some git versions have some bug where come.exe is called causing go commands to fail on windows.
To fix I just removed Cygwin from path and updated git to latest version.