Thanks Sam - I came to the same conclusion and finally got a change through to try this out today. No luck though - same problem after a repair using the new cname. Nothing else broke though (other than a little css tweaking - easily fixed) so yes it was fairly straight forward.
Its weird - everything seems to work fine except for links and image references within the Standard Report Viewer web part. Its almost as if whatever delivers these web parts is doing some sort of reverse lookup when the request is from a remote source.
For example;
Remote browser to [alias.mydomain] - links in web part refer to [servername.anotherdomain]
Local browser to [alias.mydomain] - links in web part refer to [alias.mydomain]
Local browser to [localhost] - links in web part refer to [localhost]
Local nslookup on servers IP yields [servername.anotherdomain]
I do have two domains here and yes there is another IIS server doing a domain re-write on the way through which complicates things. As far as I know, everything else is working in this setup though - other Process Manager components and various workflow forms we use.