I have an ISA server 2004 configured as firewall and proxy. Access to the Internet works fine. But accessing internal web-servers (on the LAN), is troublesome. All clients are WinXP configured as secure NAT clients.
From a clients IE, I try to access an intranet web server, by using its hostname, i.e. myweb, which works fine, no matter whether the client uses ISA for proxy, or not. When I try the same, using a FQDN, i.e. myweb.mydomain.com, it only works when the clients IE doesn't use ISA for proxy. When IE uses the proxy, response from the web server is very slow, and time outs keep occurring.
The timeouts sometimes appear as partially listed web sites, sometimes as ISA-brown-web-page-timeout with "Error Code 10060: Connection timeout Background: The gateway could not receive a timely response from the website you are trying to access"
Until you've updated the local access entries on your clients you could use a web chaining rule to redirect the requests to the internal server. Simply create a domain name set containing the fdqn of the internal server and set the web chaining rule to apply to requests to that domain name set and redirect them to the internal server.