Ok. I'm answering my own question here.
It seems FileMaker server gets very confused with two or more network cards on the same machine, and very much so if you try and force it to an IP address.
My workaround was to delete the XML files out of the admin\conf folder except the deployment.xml, disabled all but the networking card pointing to the webserver, and then opened up the admin page from http://localmachine:16000 and reconfigured the server and hey presto it's now pointing at the correct card, then I reenabled the other cards again. I also had to remove IPv6 from the cards as this seemed to give the webserver in filemaker a random IP address of 22.214.171.124 or similar, which isn't even in my networks range!
Anyway, it seems ok, just need to workout how to publish so I can test using a database through a browser :-S