diff --git b/ctools.module a/ctools.module
index 62aade9..9fef308 100644
--- b/ctools.module
+++ a/ctools.module
@@ -549,7 +549,9 @@ function ctools_cron() {
  * Implements hook_flush_caches().
  */
 function ctools_flush_caches() {
-  return array('cache_ctools_css');
+  // Only return the CSS cache bin if it has been activated, to avoid
+  // drupal_flush_all_caches() from trying to truncate a non-existing table.
+  return variable_get('cache_class_cache_ctools_css', FALSE) ? array('cache_ctools_css') : array();
 }
 
 /**