John
You were right, the cobalt server runs an extra httpd process called "ahttpd" running on port 81 and as you said runs as root.
It uses .htaccess files to protect the access so you can't just post to it to automate it in its current form and if you contact their support, surprise, surprise, they tell you it will invalidate the warranty.
This means that a PHP web server admin system can be built but using true unix native shell commands in the background, which was the whole point of this thread in the first place because that's the project i'm on at work next.
Thanks for the pointer, if you have anything you want to run by me about anything, drop me a mail to "james@computer-geek.co.uk".
Cheers
James