I have seen weirdness depending on the order you add the nodes. If the ESX(i) server was already added, then you add the vCenter, the ESX(i) node stays being a stand alone, but if you add it the opposite way, then it is put under the vCenter. The only way I have been able to fix is remove the ESX(i) node from monitoring and re-add.
My first idea would be that you need to check the credentials for vCenter and the rights in vCenter for the user that you have configured. Does that user have rights to view all ESX hosts, clusters and so on?
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