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Well, if your managed server 2 was down at time of deployment, weblogic will deploy only on MS1.
Did you checked server bea logs?do you see any deployment activity happening during that time?
Well both the nodes were active during that time, my mistake was i didn't check the logs. I have removed the nodes from cluster and again joined then into the cluster it started working fine. really not sure how it worked... :(. Anyway, your reply is appreciated.