Is there any progress to report on this issue? It's popped up for me, as well, and it's enormously frustrating.
This particular machine usually doesn't get shut down that often, so I may not have noticed it before, but it started appearing on a SuperMicro X9SCM-F after updating from 9.10.2-U2 to U3.
Latest (2.20) firmware and IPMI (3.38). If it matters, it is connected to a UPS.
When I shut down from the GUI, it *acts* as if it's shut down, so the interface says after a while "can't connect to web page blablah". Unlike with a proper reboot, when the page apparently waits for the machine to come back. This is why it took me a while to notice the machine was still on.
After an unwanted reboot, a neat shutdown is possible using the FreeNAS console setup, via IPMI or locally.
My solution for now is a rollback to 9.3.1 and everything works great. I had some other, much smaller, issues and weirdness with 9.10 so was always a bit weary, but it's a shame not to be able to use an up-to-date FreeNAS version.