The FreeNas plugin has been updated to 3.0.5675.1. I assume the FreeBSD pbi as well, though I haven't looked.
I've been running it overnight and so far it has fixed several problems on my FreeNAS 9.3 server (Xeon 1230v3):
Restarts work now - maybe I was alone in this problem, but previous versions wouldn't restart, they would always hang and I'd have to go reboot the actual Jail. Now restarts work and are nice and quick too.
The problem with Dynamic images, so far, appears to have been fixed - I get them for movies, tv, collections folders, and they appear to get updated when media is added. I'll keep an eye on them since they were a little squirrely last time.
Also so far, the problem with Mono running out of control CPU during library scans, etc. appears to have been tamped down. This is another one that I'll need to keep an eye on; I've had it run to the point where it brings down the entire jail before. Looks like Mono was updated to the newer 4.x branch too.
Syncing is improved, CPU throttling appears to be working, somewhat. It's not quite as fast as Plex (yet) and the client updates as far as progress, etc. are still lagging - it'll show a certain % (20, 30, 50) for a long time even after the sync is done - but it's definitely improved. I synced several movies to my Surface 3 for offline viewing and it's approaching the speed of Plex (and I prefer Emby overall). I don't know how well sync works on other platforms but it wasn't that great until recently on FreeNAS.
Lots of other fixes not specific to the *BSD version, read the patch notes.
If you are running this on FreeNAS you should definitely upgrade. Note that if you update from the plugin system itself it will take a while and seem to sit on 50% forever, however after about 20 minutes or so (in my case) it will complete.