I've looked at all different levels within vCenter (server, datacenter, cluster, individual VM) and there are no alarms being reported yet the alarm icon persists.
This all started when I had to shutdown my ESXi hosts and SAN for some upgrades in my dataroom. When I turned things back on I first connected to one of the ESXi hosts with the vSphere client on my desktop to power on a domain controller and then a few other VMs. I then connected to the other ESXi host and powered on a few more (but not all).
After a few minutes I logged into the VC server (yes, it's a VM at this time), connected to vCenter with the client and then powered on a few more VMs. At this point I noticed the alert icons on the previously powered on VMs.
It would seem that the "problem" is that I started the VMs from a client connected directly to a host rather than through VC.
Powering off and on the VMs does not resolve the issue.
It turns out the problem was that I powered on my ESXi hosts before my SAN so the VMs were not "fully" registered. A simple vmotion between hosts fixed the issue.
Disconnecting the VM host from the vCenter and reconnecting it also works. Obviously, when disconnecting a host you loose statistics and other data - but this works in simple scenarios.