Do the 3 ESXi hosts where this message appears have a different build number than the other 3 hosts?
This message indicates that your ESXi hosts are vulnerable to a serious vulnerability that can bypass VM isolation (see VMSA-2018-0020 ). Because it is so critical, a warning or alert is displayed.
This message were introduced in the ESXi650-201808001 and ESXi670-201808001 patches. This corresponds to build 9298722 for vSphere 6.5 and build 9484548 for vSphere 6.7.
Here you can compare the build numbers and releases: VMware Knowledge Base
To mitigate this vulnerability you have to deactivate HyperThreading via a new advanced setting (VMkernel.Boot.hyperthreadingMitigation). But since this results in CPU performance losses, VMware has provided a workflow with 3 phases and an analysis tool. See here for more information: VMware Knowledge Base
Yes that was the exact issue. I realized that a couple hours ago. The newer build has the security fix added to the advanced settings. It is default to "False" and you decide wither you want to make it "True" or not.
The other 3 are the version prior which doesn't have this vulnerability patched.
If you want to just suppress the warning and accept the risk of leaving hyperthreading enabled you can follow these instructions.