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You cant compare the memory reported in vrops to what is being reported in the OS.
The vrops memory stats does not take into consideration the application memory usage in the VM. SQL for instance will cache store procedures in memory for faster recall but that memory is not active on the hosts. The memory stat in vrops will only show you what is active on the host so you will in most cases see the vrops start much lower than the OS stats.
vrops did introduce OOTB in guest memory stats without the need for an agent. Not sure if 6.4 supports the in guest and it is also ESXi version and tools version specific someone else here will hopefully know and post the requirements
Actually the app in question is an Oracle DB and the customer did mention about having some of the allocated mem in some form of cache/reserve. The only problem here is that apparently there is a second DB server which doesn't have the same "reporting issue"