We are also pushing (via AD Group Policy) a URL to the proxy.pac file. So far, we have not had an issue with a blank file, but ....... (crosses fingers)......
The only time I've ever seen a PAC file come back blank from the appliance was when the file was editted on the file system itself and the file ownership was not set to wwasher:wwasher. For example, If the ownership is set to root:root, it will come back blank.
Also, if the file just plain doesn't exist on the directory, it will return a blank file. Also, if you have it hosted on multiple machines, I don't think it replicates automatically from a master to a site instance.
Interesting. Unfortunatley this wasnt the case. However on a good note we havent had the issue since.