I have had to do this once out of several reboots/shutdowns of my FreeNAS box. For some reason it was having trouble starting the iSCSI target and so it was failing silently on start up. Only caught it when I had the system logs displayed in the footer. A reboot didn't fix it. I had to stop and start the iSCSI service and then life was good. So I think it is a bug. But it's going to be a fun one to track down as it obviously doesn't get triggered on every reboot or shutdown. Aside from that one time, I have rebooted and shutdown the system and as long as I give the FreeNAS box ample time to start up before the ESXi box, it has no trouble seeing the iSCSI target on boot and autostarting VMs works like a charm.