diff -u b/panels.install b/panels.install
--- b/panels.install
+++ b/panels.install
@@ -448,10 +448,11 @@
   // Initialize information needed by the batch update system.
   if (!isset($sandbox['progress'])) {
     $sandbox['progress'] = 0;
-    $sandbox['max'] = db_query('SELECT COUNT(DISTINCT pd.did) FROM {panels_display} pd
+    // Must use this strange query structure to avoid this MySQL bug: http://bugs.mysql.com/bug.php?id=30402
+    $sandbox['max'] = db_query('SELECT COUNT(*) FROM (SELECT DISTINCT pd.did FROM {panels_display} pd
 LEFT JOIN {panels_pane} pp ON pp.did = pd.did
 WHERE pd.uuid  = \'\' OR pd.uuid IS NULL OR pp.uuid = \'\' OR pp.uuid IS NULL
-ORDER BY pd.did')
+ORDER BY pd.did) countalias')
       ->fetchField();
     // If there's no data, don't bother with the extra work.
     if (empty($sandbox['max'])) {