There's no great way of measuring *network* latency when a proxy server is involved. Proxy servers don't typically like to send out ICMP packets, and they're pretty good at caching results instead of sending them to a server.
That said, you may be able to make a little bit of headway in this direction by doing HTTP GET requests. You can set up the proxy information in the options dialog of PingPlotter Pro, then use the HTTP GET script
to check latency of the web server / proxy server combination. Lots of possible pitfalls here, but that's about the best we can do.