Just wanted to say that I have exactly the same choppy/lagging issues with the same setup (Shield TV etc), so I'm watching this thread with interest! :)
I did manage to fix it for a while by changing from NFS to SMB shares on my Synology NAS, but the problem has re-appeared!
But is seems as though the problem is back again now for some reason.
It's always been like this, but everything else is fine. i.e. MKV movies and TV shows that were not recorded through TVHeadEnd!
It's driving me nuts, and it's been like this for months!
Cheers
Will.