While stumbling through the chromium code documentation, I came across this post: http://code.google.com/p/chromium/wiki/UsingGit#Windows If you are using msysgit, you are asking for trouble. Using both msysgit (including TortoiseGit) and cygwin's version of git is a path to lead to repository corruption so it's safer to stick with the cygwin's version. So if you still have msysgit in your PATH, you are on your own. Does this really happen? What causes the corruption?