You didnt mention whether the proxy had been manually assigned (set in the browser config) or whether it was transparent, but I'll assume that it has been manually assigned because of the symptoms you describe. The proxy server is not "overwriting any mappings", its most likely doing its own DNS lookups. It gets a HTTP request from the client and it does the hostname to IP address translation itself. Under these circumstances it doesnt matter what IP address the client thinks the web server has.
Redirecting proxy requests to your own systems proxy server should work.