diff -u b/includes/bootstrap.inc b/includes/bootstrap.inc
--- b/includes/bootstrap.inc
+++ b/includes/bootstrap.inc
@@ -1058,7 +1058,7 @@
 }
 
 /**
- * Triggers a user-level warning for missing or unexpectedly moved files.
+ * Registers a user-level warning for missing or unexpectedly moved files.
  *
  * @param $type
  *   The type of the item (theme, theme_engine, module, profile).
@@ -1069,22 +1069,41 @@
  *
  * @see drupal_get_filename()
  * @see _drupal_get_filename_fallback()
+ * @see _drupal_get_filename_fallback_trigger_error_invoke()
+ * @see _drupal_bootstrap_full()
  */
 function _drupal_get_filename_fallback_trigger_error($type, $name, $error_type) {
   // Make sure we only show any missing or moved file errors only once per
-  // request.
-  static $errors_triggered = array();
+  // request. We delay the trigger_error to _drupal_bootstrap_full()
+  // to prevent calling watchdog early in the bootstrap.
+  $errors_triggered = &drupal_static(__FUNCTION__, array());
+
   if (empty($errors_triggered[$type][$name][$error_type])) {
-    if ($error_type == 'missing') {
-      trigger_error(format_string('The following @type is missing from the file system: %name. In order to fix this, put the @type back in its original location. For more information, see <a href="@documentation">the documentation page</a>.', array('@type' => $type, '%name' => $name, '@documentation' => 'https://www.drupal.org/node/2487215')), E_USER_WARNING);
-    }
-    elseif ($error_type == 'moved') {
-      trigger_error(format_string('The following @type has moved within the file system: %name. In order to fix this, clear caches or put the @type back in its original location. For more information, see <a href="@documentation">the documentation page</a>.', array('@type' => $type, '%name' => $name, '@documentation' => 'https://www.drupal.org/node/2487215')), E_USER_WARNING);
-    }
     $errors_triggered[$type][$name][$error_type] = TRUE;
   }
 }
 
+/**
+ * Triggers the errors that had been registered earlier.
+ *
+ * @see _drupal_get_filename_fallback_trigger_error()
+ */
+function _drupal_get_filename_fallback_trigger_error_invoke() {
+  $errors_triggered = &drupal_static('_drupal_get_filename_fallback_trigger_error', array());
+  foreach ($errors_triggered as $type => $modules) {
+    foreach ($modules as $name => $types) {
+      foreach (array_keys($types) as $error_type) {
+        if ($error_type == 'missing') {
+          trigger_error(format_string('The following @type is missing from the file system: %name. In order to fix this, put the @type back in its original location. For more information, see <a href="@documentation">the documentation page</a>.', array('@type' => $type, '%name' => $name, '@documentation' => 'https://www.drupal.org/node/2487215')), E_USER_WARNING);
+        }
+        elseif ($error_type == 'moved') {
+          trigger_error(format_string('The following @type has moved within the file system: %name. In order to fix this, clear caches or put the @type back in its original location. For more information, see <a href="@documentation">the documentation page</a>.', array('@type' => $type, '%name' => $name, '@documentation' => 'https://www.drupal.org/node/2487215')), E_USER_WARNING);
+        }
+      }
+    }
+  }
+}
+
 /**
  * Writes the file scan cache to the persistent cache.
  *
diff -u b/includes/common.inc b/includes/common.inc
--- b/includes/common.inc
+++ b/includes/common.inc
@@ -2757,7 +2757,6 @@
   _registry_check_code(REGISTRY_WRITE_LOOKUP_CACHE);
   drupal_cache_system_paths();
   module_implements_write_cache();
-  drupal_file_scan_write_cache();
   system_run_automated_cron();
 }
 
@@ -2768,6 +2767,7 @@
   _registry_check_code(REGISTRY_WRITE_LOOKUP_CACHE);
   drupal_cache_system_paths();
   module_implements_write_cache();
+  drupal_file_scan_write_cache();
   system_run_automated_cron();
 }
 
@@ -5270,6 +5270,8 @@
     drupal_theme_initialize();
     module_invoke_all('init');
   }
+
+  _drupal_get_filename_fallback_trigger_error_invoke();
 }
 
 /**