mysqldump --flush-logs not working

[Chris Isaksen]

MySQL version 5.6.10, databases are InnoDB
I'm having some strange behavior from mysqldump. Here is the command:

mysqldump \
--protocol=tcp \
--port=3320 \
--host=${host} \
--user=backupdba \ ## backupdba has select, reload and replication on *.*
--password=${pwd} \
--single-transaction \
--flush-logs \
--all-databases \
> outputfile.sql

Binary logging in enabled.
Like this the command ony produces a sql dump with very basic info.
-- MySQL dump 10.13 Distrib 5.6.10, for Linux (x86_64)
--
-- Host: <hostname> Database:
-- ------------------------------------------------------
-- Server version 5.6.10-log

/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
/*!40101 SET NAMES utf8 */;
/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */;
/*!40103 SET TIME_ZONE='+00:00' */;
/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */;
/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */;
/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */;
/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;
/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */;

/*!40101 SET SQL_MODE=@OLD_SQL_MODE */;
/*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */;
/*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */;
/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;

-- Dump completed on 2013-11-13 8:37:25

Now if I remove the --flush-logs I get a successfully dump with everything included. Not sure why this is happening. I have an exact duplicate DB on another server and that works just fine with the --flush-logs in the dump command. Even all the variables are exactly the same.

Any ideas ? Not really sure where to go as I don't even get any errors even with verbose and debug on.
Thanks