Ok so I figured out why I am getting the same error on reinstall. I was only making the changes to the ram version and was not installing it to disk. :o The only issue then was the error on upgrade where the upgrade would fail on reboot with the error described. "Launching inti system ...flock. Could not execute /usr/local/etc/rc.bootup". It was strange because the file was there. When I tried running "php /usr/local/etc/rc.boottup" Php could not be found.