I have the same Problem, also flickering on starting a Video, but not with all files. Have you found a solution? Setting the refresh rate to 50hz leaves me with a black screen.
I have a similar problem with my ambilight. I use Hyperion on my raspberry pi 3. Since the update to libreelec 8 not the light flickers but the video itself flickers if i have hyperion turned on. If i turn it of the flickering is gone. Maybe the problem is related to yours, sadly i couldn't find e solution yet.