Hi Anthony,
Yes the URL has been applied as a root URL. The site loads with the proxy address in the url bar - but all links under the site still use squiz.blah/sitename- our tech guys said it looked as if Squiz maybe wasn't respecting the X-FORWARDED-HOST header to retain the proxied address in its links.
Matrix only looks at the "host" header (not "X-Forwarded-Host") as such it only currently supports proxies that pass through the host header unmodified (e.g. Squid, Varnish, mod_proxy).
In more detail the fact that your tech guy is mentioning "X-Forwarded-Host" suggests they want the client to connect to the proxy on proxy.example.com (with a host header of "proxy.example.com") and then have the proxy forward that connection on with a host header of "matrix.example.com" (whatever the DNS name the proxy is connecting to Matrix on) and a "X-Forwarded-Host" header of "proxy.example.com".
Because Matrix is ignoring the "X-Forwarded-Host" header you will end up getting links calculated from the hostname ("matrix.example.com") of the Matrix install rather than the domain name the client is connecting to. This type of behaviour can be confirmed by adding a Root URL and a Site Asset with the hostname the proxy is connecting to in Matrix and seeing if connecting via the proxy starts showing that instead.
Ideally you can talk to your tech guys to turn off "X-Forwarded-Host" (e.g. with mod_proxy you would turn on ProxyPreserveHost: http://httpd.apache.org/docs/2.2/mod/mod_proxy.html#proxypreservehost).