Dude, are you sure that you need 1000v? We also wanted to deploy it in our infrastructure. Moreover I successfully installed it in test environment and tested it. But later we realized that it's no longer supported and it will not be developed by Cisco as I know because of some disagreements between Cisco and VMware (at least I heard it from tutor on authorized courses). Do you really need to deploy this almost dead stuff in your environment? We finally decided to use original vmware vDS. As I know there are analogs of Nexus from IBM and other vendors.
As for your question, did you install correct versions of VEM of ESXi hosts? I didn't remember clearly but I suppose we had similar problem.