i was having the same issue. My all-in-one system worked beautifully in esxi 5.0, ok-ish in 5.5, but 6.0 seems to hate not seeing the iscsi "drives" and doesn't handle that very well. I ended up moving my vm images to a separate drive (an ssd) outside of FreeNAS, and redesigned my VMs so that they have smaller system drives, but store most of their data on network shares. Esxi all-in-ones are a PITA.great ... converted to iSCSI ... left server rebooting overnight, the iSCSI datastore never refreshed even after hours. only way is to "rescan" volumes manually after boot.
This bypasses the whole chicken and egg thing with esxi not seeing iscsi drives upon bootup and failing to bit my vms. I've tried playing with delays, scripts, then just decided that my time and sanity are worth more than the cost of an ssd.