Last week I ran into a VMFS version warning message while building a new vSphere 6 environment for a enterprise customer. This environment is a green field deployment, so everything is new from SAN infrastructure, Network, Compute and Storage.
When I started adding payload ESXi hosts to their respective HA clusters, the only warning message I received was about the System logs being stored on non-persistent storage. This was expected as the hosts where Blades (without any local harddisks) which booted the hypervisor of a embedded USB device and there was no shared storage available yet.
After presenting shared storage and adding it to the ESXi hosts, being formatted in the process as VMFS 5 (VMFS 5.61 to be exact) all looked fine.
But when I rebooted the ESXi hosts, they came back online within vCenter and there was a extra warning message: Deprecated VMFS volume(s) found on the host. Please consider upgrading volume(s) to the latest version
Not sure if deploying the EMC OVA had anything to do with the warning message. In any case VMware has a KB article about the false positive deprecated VMFS warning.
KB2109735 does not disclose what is causing this false positive, but it does suggest a simple yet effective solution to the problem. At least it did solve the problem in my case.
By restarting the hosts management services the warning message is gone, the easiest way to do this is to run services.sh restart from either the DCUI or through a SSH session.