Well, after yesterdays hassle I noticed a few other things that didn't seem to be working right so I thought I'd setup a new install on another machine just to confirm whether it was what I did yesterday or not.
After completing installation of 3.16.0 with out any errors and following the installation guide religiously, I'm getting some Forbidden errors when trying to run HIPO tasks. The same thing is happening in my original system which is why I tried a different machine.
My apache error_log displays the following
[Thu Sep 6 14:19:54 2007] [error] [client 139.80.9.64] client denied by server configuration: /Library/WebServer/dcc_matrix/core/web/index.php
[Thu Sep 6 14:19:54 2007] [error] [client 139.80.9.64] client denied by server configuration: /Library/WebServer/dcc_matrix/core/web/index.php
[Thu Sep 6 14:21:13 2007] [error] [client 139.80.9.64] client denied by server configuration: /Library/WebServer/dcc_matrix/core/web/index.php
The bizarre thing is that it isn't consistent when it appears and if I quit the browser and reopen and go into the admin interface, I can restart the job in the HIPO herder and it will sometimes complete with out any errors or it will get a bit further before giving me a 403 error again.
My vhost setup is a copy and paste of the install instructions with my directory paths updated.
Update: Also just noted in Safari that I have little red circles with a white cross on all root assets (Designs, Media, Users, System Management) apart from my test site and trash when logged in as root.