ok. The problem I have seen on a number of deployments now is that when you manually put in the proxy settings into the device, like iPhone iPad, system apps like Safari work, but many many other 3rd party apps don't use these proxy settings, and fail.
I suspect what you are seeing is similar in that they are ignoring the proxy settings obtained from the pac file.
How we got around that is for the upstream firewall to do the filtering, or for it to dst-nat to a transparent proxy.