Clustering: Recovery misses flows installed

Steps to reproduce
1. Create an OFP distribution on master
2. Start the controller install odl-openflowplugin-all
3. Connect mininet - sudo mn --controller=remote,ip=<host> --topo tree,3
4. Run config flow blaster a couple of times
./flow_config_blaster.py --auth --threads 5 --flows 5000 --no-delete
5. Check the number of flows in config and note the number
5. Stop controller gracefully.
6. Stop mininet
7. Start the controller
8. Connect mininet
9. Check the number of flows in config. Around 400 are missing.

The log is filled with messages :

2015-05-18 14:07:20,796 | INFO | lt-dispatcher-25 | Shard | 175 - org.opendaylight.controller.sal-akka-raft - 1.2.0.SNAPSHOT | Recovery snapshot applied for member-1-shard-inventory-config in 2.119 s: snapshotIndex=39999, snapshotTerm=1, journal-size=0
2015-05-18 14:07:20,805 | INFO | lt-dispatcher-25 | Shard | 175 - org.opendaylight.controller.sal-akka-raft - 1.2.0.SNAPSHOT | member-1-shard-inventory-config: Received ReplicatedLogEntry for recovery: index: 40322, size: 1445
2015-05-18 14:07:20,806 | INFO | lt-dispatcher-25 | Shard | 175 - org.opendaylight.controller.sal-akka-raft - 1.2.0.SNAPSHOT | member-1-shard-inventory-config: Received ReplicatedLogEntry for recovery: index: 40323, size: 1441
2015-05-18 14:07:20,806 | INFO | lt-dispatcher-25 | Shard | 175 - org.opendaylight.controller.sal-akka-raft - 1.2.0.SNAPSHOT | member-1-shard-inventory-config: Received ReplicatedLogEntry for recovery: index: 40324, size: 1441
2015-05-18 14:07:20,806 | INFO | lt-dispatcher-25 | Shard | 175 - org.opendaylight.controller.sal-akka-raft - 1.2.0.SNAPSHOT | member-1-shard-inventory-config: Received ReplicatedLogEntry for recovery: index: 40325, size: 1445
2015-05-18 14:07:20,807 | INFO | lt-dispatcher-25 | Shard | 175 - org.opendaylight.controller.sal-akka-raft - 1.2.0.SNAPSHOT | member-1-shard-inventory-config: Received apply journal entries for recovery, applying to state: 40000 to 40322
2015-05-18 14:07:20,813 | ERROR | lt-dispatcher-25 | Shard | 175 - org.opendaylight.controller.sal-akka-raft - 1.2.0.SNAPSHOT | Log entry not found for index 40004
2015-05-18 14:07:20,813 | INFO | lt-dispatcher-25 | Shard | 175 - org.opendaylight.controller.sal-akka-raft - 1.2.0.SNAPSHOT | member-1-shard-inventory-config: Received apply journal entries for recovery, applying to state: 40004 to 40323
2015-05-18 14:07:20,814 | ERROR | lt-dispatcher-25 | Shard | 175 - org.opendaylight.controller.sal-akka-raft - 1.2.0.SNAPSHOT | Log entry not found for index 40004
2015-05-18 14:07:20,814 | INFO | lt-dispatcher-25 | Shard | 175 - org.opendaylight.controller.sal-akka-raft - 1.2.0.SNAPSHOT | member-1-shard-inventory-config: Received apply journal entries for recovery, applying to state: 40004 to 40324
2015-05-18 14:07:20,814 | ERROR | lt-dispatcher-25 | Shard | 175 - org.opendaylight.controller.sal-akka-raft - 1.2.0.SNAPSHOT | Log entry not found for index 40004
2015-05-18 14:07:20,814 | INFO | lt-dispatcher-25 | Shard | 175 - org.opendaylight.controller.sal-akka-raft - 1.2.0.SNAPSHOT | member-1-shard-inventory-config: Received apply journal entries for recovery, applying to state: 40004 to 40325
2015-05-18 14:07:20,814 | ERROR | lt-dispatcher-25 | Shard | 175 - org.opendaylight.controller.sal-akka-raft - 1.2.0.SNAPSHOT | Log entry not found for index 40004
2015-05-18 14:07:20,814 | INFO | lt-dispatcher-25 | Shard | 175 - org.opendaylight.controller.sal-akka-raft - 1.2.0.SNAPSHOT | member-1-shard-inventory-config: Received ReplicatedLogEntry for recovery: index: 40326, size: 1441
2015-05-18 14:07:20,814 | INFO | lt-dispatcher-25 | Shard | 175 - org.opendaylight.controller.sal-akka-raft - 1.2.0.SNAPSHOT | member-1-shard-inventory-config: Received apply journal entries for recovery, applying to state: 40004 to 40326
2015-05-18 14:07:20,814 | ERROR | lt-dispatcher-25 | Shard | 175 - org.opendaylight.controller.sal-akka-raft - 1.2.0.SNAPSHOT | Log entry not found for index 40005
2015-05-18 14:07:20,814 | INFO | lt-dispatcher-25 | Shard | 175 - org.opendaylight.controller.sal-akka-raft - 1.2.0.SNAPSHOT | member-1-shard-inventory-config: Received ReplicatedLogEntry for recovery: index: 40327, size: 1445

The snapshot was taken at index=39999 with 0 unapplied entries.
The persistent journal starts with the index=40322.
Where did the 322 logs go?