What client configuration are you running and why?
We are using AD Group Policy to force a PAC configuraiton that points to a network location that the PAC is located. We are running this configuration to allow us to quickly update also have a dynamic failover to the other appliances in our environment.
The reason I bring this up is our configuration caused a failure yesterday because the appliance was hosting a blank PAC file.
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.