I'm not sure what problems the author had with Cygwin that he didn't with Git's msys environment. I'm not denying that there were problems, I'm just curious what they were.
I guess the problems come once anybody tries to mix the environments at once: Git installs msys, the user additionally installs Cygwin and if both are in the path the confusion is certain.
Is there a problem simply using the version of git that comes with Cygwin? Seems to work for me.