I'm upgrading my ISA 2004 server to ISA 2006 on a different server. The 2006 server is running fine but I have come across a few instances on where I can't access certain pages through 2006 but when I point my proxy address to the 2004 server the page works.
The only real difference I see between the two servers are the firewall policies I created for the proxy users. The protocols I applied for the 2006 proxy server rules are HTTP, HTTPS, and FTP.
The protocols that are enabled for the 2004 proxy server rules are HTTP, HTTPS, FTP, DNS, RPC, Telnet, Time, and bunch of different Kerberos, LDAP, Netbios protocols.
I didn't apply all of those protocols for 2006 because I wasn't sure if they were needed. I did not build our 2004 server.