I have the problem too but only with files from itunes. Since I am able to recreate the problem on a different Kodi system (nvidia shield), I believe that the problem is with Kodi. Vdeo starts normally for about 10 seconds, then goes black for a second and continues normally. It kind of feels like the refresh rate is changed again because it just looks the black out at the start of the movie when refresh rate is switched from 60hz to 23.976… it sometimes happens later in the movie as well,
It is not a big problem and I identified that the problem is with itunes movie files, so I kind of know what will happen, so I either avoid those files or just live with it. But it sounds very similiar to what people are reporting here.