Heads up to other people: when you were looking for a solution to your site being broken at random while having this bugged CloudFlare plugin version, you might’ve saved some options, for example in WP Super Cache. Since the sanitization (urlencode) of all POST and GET vars was turned on, when saving the WP Super Cache settings, it broke the cache directory set in /wp-content/wp-cache-config.php and you have to set it manually to:
$cache_path = WP_CONTENT_DIR . '/cache/';
Check for other stuff which you might’ve broken along the way of trying to fix this.
@jwineman, I assume you’re not sanitizing all the POST and GET vars any more with the new version?