I have reinstalled ISPConfig 3 completely - ran uninstall -q uninstall.php and then reinstalled.
The result is the same as before - add one site and the system is happy - I modify the index.html file in the /var/clients/client?/web?/web folder as a check. Add second site and it reflects exactly the same file?
I am sure that this is not the way it is meant to be? Please could someone confirm, thank you.