Thank you for the logs. I'm noticing that times on agent VMs and appd server are out of sync. Can you make sure they are same (at-least roughly)?
From the logs Jun 03 2013 16:41:57 on agent seems to be same as Jun 03 2013 19:51:23 on the server. So there is over 3-hour drift between them.
One way to converge on the same time is to use the same time source (say NTP). Configure your hypervisors hosting application vms and appd vm to refer to the same time source.
Thanks Rags