diff -u b/includes/common.inc b/includes/common.inc
--- b/includes/common.inc
+++ b/includes/common.inc
@@ -4428,7 +4428,7 @@
           // See drupal_add_js() for details.
           $key = 'aggregate_' . $item['group'] . '_' . $item['every_page'] . '_' . $index;
           $processed[$key] = '';
-          $files[$key][$item['data']] = $item;
+          $aggregate_files[$key][$item['data']] = $item;
         }
         break;
 
@@ -4445,8 +4445,8 @@
   }
 
   // Aggregate any remaining JS files that haven't already been output.
-  if ($preprocess_js && count($files) > 0) {
-    foreach ($files as $key => $file_set) {
+  if ($preprocess_js && count($aggregate_files) > 0) {
+    foreach ($aggregate_files as $key => $file_set) {
       $uri = drupal_build_js_cache($file_set);
       // Only include the file if was written successfully. Errors are logged
       // using watchdog.
@@ -4456,6 +4456,9 @@
         $js_element['#attributes']['src'] = $preprocess_file;
         $processed[$key] = theme('html_tag', array('element' => $js_element));
       }
+      else {
+        unset($processed[$key]);
+      }
     }
   }
 
@@ -5004,9 +5007,16 @@
     foreach ($files as $path => $info) {
       if ($info['preprocess']) {
         // Append a ';' and a newline after each JS file to prevent them from running together.
-        $contents .= file_get_contents($path) . ";\n";
+        if ($content = file_get_contents($path)) {
+          $contents .= $content . ";\n";
+        }
       }
     }
+
+    // Return if there's no content.
+    if (empty($contents)) {
+      return FALSE;
+    }
     // Prefix filename to prevent blocking by firewalls which reject files
     // starting with "ad*".
     $filename = 'js_' . drupal_hash_base64($contents) . '.js';