Thanks for the report. Could you apply this patch and confirm it is working for you?

Fixes #4156 Adding ORDER BY clause when DELETING so that it works with replication
https://dev.mysql.com/doc/refman/5.1/en/replication-features-limit.html
(cherry picked from commit ce6254e)

1 files changed, 6 insertions, 2 deletions

diff --git a/core/Db.php b/core/Db.php
index ef2f756f9d..a8369943ba 100644
--- a/core/Db.php
+++ b/core/Db.php
@@ -156,11 +156,15 @@ class Db
      * @param string $where            The where clause of the query. Must include the WHERE keyword.
      * @param int $maxRowsPerQuery  The maximum number of rows to delete per DELETE query.
      * @param array $parameters       Parameters to bind in the query.
+     * @param string $primaryKey Name of primary key to sort by.
      * @return int  The total number of rows deleted.
      */
-    static public function deleteAllRows($table, $where, $maxRowsPerQuery = 100000, $parameters = array())
+    static public function deleteAllRows($table, $where, $orderBy, $maxRowsPerQuery = 100000, $parameters = array())
     {
-        $sql = "DELETE FROM $table $where LIMIT " . (int)$maxRowsPerQuery;
+        $sql = "DELETE FROM $table
+                $where
+                ORDER BY $orderBy ASC
+                LIMIT " . (int)$maxRowsPerQuery;
 
         // delete rows w/ a limit
         $totalRowsDeleted = 0;