diff -u b/includes/bootstrap.inc b/includes/bootstrap.inc
--- b/includes/bootstrap.inc
+++ b/includes/bootstrap.inc
@@ -845,4 +845,8 @@
   static $files = array();
 
+  // This flag may hold a string that indicates where the filename was retrieved
+  // from.
+  $filename_retrieved_from = '';
+
   // Profiles are a special case: they have a fixed location and naming.
   if ($type == 'profile') {
@@ -856,6 +860,7 @@
   if (!empty($filename) && file_exists($filename)) {
     // Prime the static cache with the provided filename.
     $files[$type][$name] = $filename;
+    $filename_retrieved_from = 'priming';
   }
   elseif (isset($files[$type][$name])) {
     // This item had already been found earlier in the request, either through
@@ -864,34 +869,40 @@
     // Do nothing.
   }
   else {
-    $system_filepaths = &drupal_static('system_filepaths');
-    if (!isset($system_filepaths[$type][$name])) {
-      // Look for the filename listed in the {system} table.
-      // Verify that we have an active database connection, before querying
-      // the database. This is required because this function is called both
-      // before we have a database connection (i.e. during installation) and
-      // when a database connection fails.
-      try {
-        if (function_exists('db_query')) {
-          $file = db_query("SELECT filename FROM {system} WHERE name = :name AND type = :type", array(
-            ':name' => $name,
-            ':type' => $type
-          ))->fetchField();
-          if ($file !== FALSE) {
-            $system_filepaths[$type][$name] = $file;
-            if (file_exists(DRUPAL_ROOT . '/' . $file)) {
-              $files[$type][$name] = $file;
-            }
+    // Look for the filename listed in the {system} table.
+    // Verify that we have an active database connection, before querying
+    // the database. This is required because this function is called both
+    // before we have a database connection (i.e. during installation) and
+    // when a database connection fails.
+    try {
+      $system_query_success = FALSE;
+      if (function_exists('db_query')) {
+        $file = db_query("SELECT filename FROM {system} WHERE name = :name AND type = :type", array(
+          ':name' => $name,
+          ':type' => $type
+        ))->fetchField();
+        if ($file !== FALSE) {
+          if (file_exists(DRUPAL_ROOT . '/' . $file)) {
+            $files[$type][$name] = $file;
+            $filename_retrieved_from = 'system_table';
           }
         }
+        $system_query_success = TRUE;
       }
-      catch (Exception $e) {
-        // The database table may not exist because Drupal is not yet installed,
-        // the database might be down, or we may have done a non-database cache
-        // flush while $conf['page_cache_without_database'] = TRUE and
-        // $conf['page_cache_invoke_hooks'] = TRUE. We have a fallback for these
-        // cases so we hide the error completely.
-      }
+    }
+    catch (Exception $e) {
+      // The database table may not exist because Drupal is not yet installed,
+      // the database might be down, or we may have done a non-database cache
+      // flush while $conf['page_cache_without_database'] = TRUE and
+      // $conf['page_cache_invoke_hooks'] = TRUE. We have a fallback for these
+      // cases so we hide the error completely.
+      // We also hide the trigger_error() "moved or newly introduced" warning
+      // in this case as we can't be sure if it's correct.
+    }
+    if (!$system_query_success) {
+      // We can't tell if the error message will be valid if the query to the
+      // {system} table failed, so skip triggering of errors.
+      $trigger_error = FALSE;
     }
     // Fall back to searching the filesystem if the database could not find the
     // file or the file does not exist at the path returned by the database.
@@ -902,10 +913,19 @@
 
   if (isset($files[$type][$name])) {
     // We found a file.
+    // Get the static file scan list. This list may be incomplete as there
+    // may be further files listed in persistent cache, but we skip loading that
+    // as a performance optimization, as the persistent cache record will
+    // be cleared on every system_rebuild_module_data() anyway.
     $file_scans = &drupal_static('_drupal_get_filename_fallback');
     // If this file had previously been marked as missing, clean up the entry
     // from the file scan cache.
-    if (isset($file_scans[$type][$name]) && $file_scans[$type][$name] === FALSE) {
+    $missing_reappeared = isset($file_scans[$type][$name]) && $file_scans[$type][$name] === FALSE;
+    // If this file had previously been marked as moved, and reappeared
+    // at the location listed in the system table or in the primed static,
+    // clean up the entry from the file scan cache.
+    $moved_reappeared = isset($file_scans[$type][$name]) && is_string($file_scans[$type][$name]) && ($filename_retrieved_from == 'system_table' || $filename_retrieved_from == 'priming');
+    if ($missing_reappeared || $moved_reappeared) {
       $file_scans[$type][$name] = NULL;
       $file_scans['#write_cache'] = TRUE;
     }
@@ -937,7 +957,7 @@
   // keys the type and name of the item, and as value:
   // - the boolean FALSE if the item is missing
   // - a string with location found in a file scan if the module/theme has moved
-  // from the location listed in the {system} table.
+  //   from the location listed in the {system} table.
   $file_scans = &drupal_static('_drupal_get_filename_fallback');
   if (!isset($file_scans)) {
     $file_scans = array();
@@ -964,8 +984,8 @@
     }
   }
 
-  // Check whether this file had previously moved from the path listed in the
-  // {system} table.
+  // Check whether this file had moved from the path listed in the {system}
+  // table during a previous file scan.
   if (isset($file_scans[$type][$name]) && is_string($file_scans[$type][$name]) && file_exists($file_scans[$type][$name])) {
     // The file exists at the location cached in a previous file scan.
     $filename_from_file_scan = $file_scans[$type][$name];
@@ -976,22 +996,22 @@
   }
 
   if (isset($filename_from_file_scan)) {
-    // Check whether the file we found was listed as being in another
-    // location in the {system} table.
-    $system_filepaths = &drupal_static('system_filepaths');
-    if (isset($system_filepaths[$type][$name]) && $system_filepaths[$type][$name] != $filename_from_file_scan) {
-      // Make sure our change to the file scan cache will be written to
-      // the persistent cache.
-      if (!isset($file_scans[$type][$name]) || isset($file_scans[$type][$name]) && $file_scans[$type][$name] != $filename_from_file_scan) {
-        $file_scans['#write_cache'] = TRUE;
-      }
-      // This file has moved. Store its new location in the file scan cache.
+    // The file has either moved from the location in the {system} table
+    // or is not yet listed in the {system} table.
+    // Make sure our change to the file scan cache will be written to the
+    // persistent cache.
+    if (!isset($file_scans[$type][$name]) || isset($file_scans[$type][$name]) && $file_scans[$type][$name] != $filename_from_file_scan) {
       $file_scans[$type][$name] = $filename_from_file_scan;
-      // Create a user-level warning about the moved file.
-      if ($trigger_error) {
-        _drupal_get_filename_fallback_trigger_error($type, $name, 'moved');
+      if (!$trigger_error) {
+        // If we skip error triggering, do not write the found file location to
+        // persistent cache.
+        $file_scans['#write_cache'] = TRUE;
       }
     }
+    // Create a user-level warning about the moved / recently introduced file.
+    if ($trigger_error) {
+      _drupal_get_filename_fallback_trigger_error($type, $name, 'moved');
+    }
     return $filename_from_file_scan;
   }
   else {
@@ -1023,14 +1043,15 @@
  *   The type of the error ('missing' or 'moved').
  */
 function _drupal_get_filename_fallback_trigger_error($type, $name, $error_type) {
-  // Make sure we only show any missing/moved file error only once per request.
+  // Make sure we only show any missing / moved file error only once per
+  // request.
   static $errors_triggered = array();
   if (empty($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 file back in its original location or uninstall the module. 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);
+      trigger_error(format_string('The following @type is missing from the file system: %name. In order to fix this, put the file back in its original location or uninstall the module. 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 file 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);
+      trigger_error(format_string('The following @type has moved or has recently appeared within the file system: %name. In order to fix this, clear caches or put the file 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;
   }
@@ -1105,8 +1126,8 @@
   }
   $file_scans = &drupal_static('_drupal_get_filename_fallback');
   if (isset($file_scans['#write_cache'])) {
-    // Merge the newly found out missing and moved file data with
-    // the previously existing data, if we had not done so yet.
+    // Merge the newly found out missing and moved file data with the previously
+    // existing data, if we had not done so yet.
     if (!isset($file_scans['#cache_merge_done'])) {
       $cache = cache_get('_drupal_get_filename_fallback', 'cache_bootstrap');
       if (isset($cache->data)) {
diff -u b/includes/module.inc b/includes/module.inc
--- b/includes/module.inc
+++ b/includes/module.inc
@@ -121,7 +121,6 @@
  */
 function system_list($type) {
   $lists = &drupal_static(__FUNCTION__);
-  $system_filepaths = &drupal_static('system_filepaths');
 
   // For bootstrap modules, attempt to fetch the list from cache if possible.
   // if not fetch only the required information to fire bootstrap hooks
@@ -210,10 +209,7 @@
       cache_set('system_list', $lists, 'cache_bootstrap');
     }
     foreach ($lists['filepaths'] as $item) {
-      // Save the file paths from the database into a static variable so we
-      // can determine later if the files have moved.
-      $system_filepaths[$item['type']][$item['name']] = $item['filepath'];
-      // To avoid a separate database lookup for the filepath, prime the
+      // To avoid a separate database lookup for the file path, prime the
       // drupal_get_filename() static cache with all enabled modules and all
       // themes.
       drupal_get_filename($item['type'], $item['name'], $item['filepath']);
diff -u b/includes/update.inc b/includes/update.inc
--- b/includes/update.inc
+++ b/includes/update.inc
@@ -797,7 +797,7 @@
 
   // 'Default' profile has been renamed to 'Standard' in D7.
   // We change the profile here to prevent a broken record in the system table.
-  // @see system_update_7049()
+  // See system_update_7049()
   if ($profile == 'default') {
     $profile = 'standard';
     variable_set('install_profile', $profile);