Chrome is more strict than IE in dealing with PAC files. So you may (and I did) have a PAC file that works in IE, but is ignored by Chrome. To see what proxy file chrome is gathering, and hopefully an error to point you to why it’s being ignored, load this in chrome:
From here you can reload the proxy, and see what file is being pulled down. After you try to browse to a page, you can also click the link to events to hopefully find a useful error.