Donncha O Caoimh on "[Plugin: WP Super Cache] PHP Warning re missing array / wp-cache-phase2.php"

Did you check the contents of the second parameter, it should be this (taken from the config file wp-content/wp-cache-config.php)

$cache_acceptable_files = array( 'wp-comments-popup.php', 'wp-links-opml.php', 'wp-locations.php' );