sHistory: Site was built in a development location using sub-folders on first site. When moved WP Super Cache persisted in trying to read the old locations. Despite code changes etc. a solution could not be found. That plugin was deactivated and deleted.
However when i tried to activate W3 Total Cache, it raised the same errors. Its adding /var/www/oldDirectory/ at the start of all the directories it should be using and failing. This is essentially the same error that WP Super Cache was raising once the site was moved.