What kind of time server do you use? There are known issues with Windows Domain Controllers (see VMware KB: Synchronizing ESXi/ESX time with a Microsoft Domain Controller ). You may also want to ensure that the time server isn't a VM running on one of these hosts. Do you have direct network access to the time server, or through a proxy?
The NTP servers are on the same subnet and are a Cisco 1841 Router and a Cisco Catalyst 3550 Switch. Other systems in the environment (Websense Appliance, Linux, Windows, etc) use it to sync time with no issues.
just from VMware perspective if you want to entirely stop any VM to sync it's time with underlying host and be sure that virtualization layer is not
the cause of similar issues you have to manualy edit .vmx files of all affected VMs otherwise operations like (Power On, vMotion, Suspend, Snapshots)
will force time sync with the host even you have unchecked time sync checkbox in VMtools options.
All the settings are described in this KB article:_________________________________________________________________________________________
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Do not use time from ESXi for VMs, use from PDC for this you have to uncheck the time sync option in the VM options