Cool, I'm glad it's working out for you. Due to my workflow at my current job I haven't actually had much occasion to use it since writing it, so I'm not that confident about how good the hueristics are.
Do you generally use the default --strict setting?
git-autofixup can also be installed by simply downloading the script[1], giving it execute permissions, and putting it somewhere in your PATH. It needs perl 5.8.4+, which is very old, and only depends on the standard library. Git ships with a Perl interpreter on Windows.
If there are any staged changes, git-autofixup only fixes those up and ignores any unstaged ones; otherwise it tries to autofixup all unstaged changes.
Do you generally use the default --strict setting?