I managed to figure several things about. For whatever reason, my install of lighty hates serving things from the /var/www/ directory. This is rectified by re-writing everything something like /home/whatever directory.
Secondly, if the permissions are set to anything other than 777 for the board root directory the script will refuse to write them. 775 755 etc do not work. I'll dig around more and see if I can find anything as to why this is the case.
Thanks for your help guys.