I had similar experience (also ubuntu 16.04 LTS) so I downgraded to ffmpeg to 3.4.4. It would sometimes completely freeze my Rpi2 with Libreelec / Kodi / PVR HTS client that it had to be power cycled.
I removed the ppa and ffmpeg 4.*
sudo apt-get install ppa-purge && sudo ppa-purge ppa:jonathonf/ffmpeg-4
I added the ppa for ffmpeg 3.* and updated the stock ffmpeg
sudo add-apt-repository ppa:jonathonf/ffmpeg-3
sudo apt-get update
After a couple of hours of testing with various stream sources it seems that the stuttering and freezing has gone.
Hope this helps