I'm having the same problem. Everything is updated and happens on almost every video playback. YouTube, Twitch or even Stream.cz have the same problem.
I'm using 46.0.2597.11 (PGO) and even though it is Opera Beta, I am responding here, because unfortunately I haven't found topic discussing this problem in Beta and Developer subforum.
My screen resolution is 1080p60hz as well
I haven't changed any flags settings regarding media playback so far (only the one which in previous Beta build caused media not playing at all)