I ended up calling Apple Support on this one.
It turns out that a short term network conf change due to unpluging ethernet and enabling of Wi-Fi had resulted in a (automatic) hostname change for the duration of the network conf change. The hostname change had screwed around with the conf of many of the services I had set up. Whilst I had managed to fix DNS and Open Directory all the web enabled stuff was broken and the more I played with the conf the worse it got.
The solution to get all the web stuff working again was:
1. Turn off all web services (i.e. Web, Wiki, Profile Mgr) in Server app.
2. For all Shared Folders disable WebDav (i.e. uncheck share via WebDav option) in Server app
3. In Terminal window execute the command "sudo serveradmin command web:command=restoreFactorySettings"
4. Turn Web back on again in Server app.
5. Turn Wiki and Profile Manager back on in Server app
6. Re-enable all your WebDav shares.
Should now be working again.
I was told by the support guy to ensure that the network conf does not change again (i.e. the main IP address must now remain the same) to prevent it happening again. There is no way to prevent the automatic hostname change and subsequent "damage" if you start playing around with the network interfaces.
Hope this helps.