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Replication WAN Issue

We recently updated our core at our DR facility to 6.2.1.100.  Our main facility is at 6.3.1.100.  We replicate roughly 100 servers at night.  Since we upgraded to 6.2.1.100 we noticed that our replication is taking an extra hour to hour and a half to complete.  Network graphs show that we are not using 100% of the WAN connection when we replicate at night.  The connection will go up and then it looks like before it starts the next server replication the connection stops and waits and then starts the next server.  If we replicate one server with a large amount of data the software uses the entire WAN connection for that one server.  We have never had an issue with this prior to upgrading DR.  Our nightly replication always used 100% of the WAN connection until all servers we replicated to DR.  We didn't make any configuration changes to the network or to the backup settings when we upgraded to this new version but we now have encountered this issue.  Can anyone give me any thoughts on this?