diff -u b/configuration.module b/configuration.module
--- b/configuration.module
+++ b/configuration.module
@@ -1094,7 +1094,7 @@
  * @param $component
  *   The type of component, i.e node, user_permissions, taxonomy.
  * @param $identifier
- *   The identifier for the componenet, usually the machine name.
+ *   The identifier for the component, usually the machine name.
  * @param $items
  *   Items from the activestore.
  * @param $items_code
@@ -1113,21 +1113,16 @@
   $md5_activestore = (is_array($items) && array_key_exists($identifier, $items)) ? md5(serialize($items[$identifier])) : '';
 
   // Configs in code are not the same as what was just saved in activestore.
-  if ($from_activestore == TRUE && $md5_datastore != $md5_activestore) {
-    $status = $status | CONFIGURATION_ACTIVESTORE_OVERRIDDEN;
-    configuration_set_status($component, $identifier, $status);
+  if ($md5_datastore != $md5_activestore) {
+    $status = ($from_activestore == TRUE) ? $status | CONFIGURATION_ACTIVESTORE_OVERRIDDEN : $status | CONFIGURATION_DATASTORE_OVERRIDDEN;
   }
   // Config in the activestore is the same as what is in code.
-  if ($md5_activestore == $md5_datastore) {
+  else {
     $status = CONFIGURATION_IN_SYNC;
-    configuration_set_status($component, $identifier, $status);
     configuration_set_hash($component, $identifier, $md5_activestore);
   }
+  configuration_set_status($component, $identifier, $status);
 
-  if ($md5_activestore != $md5_datastore) {
-    $status = $status | CONFIGURATION_DATASTORE_OVERRIDDEN;
-    configuration_set_status($component, $identifier, $status);
-  }
   // When checking for new configurations, check to see if configurations are
   // the same in datastore as last activestore. Remove the datastore overridden.
   if ($md5_datastore == $config[$component][$identifier]['hash']) {
@@ -1149 +1144 @@
-}
\ No newline at end of file
+}