One of the reason may be inconsistency of specified segment duration and framerate/keyframe pair. You should try to keep at least 3 keyframes per segment. E.g. if you specify segment duration 5 sec and keyframe 15 fps, the keyframe parameter should not be greater than 25, so we have at least one keyframe per every 25 frames, and there are about 3 keyframes per segment (it's duration is 15*5 = 75 frames).
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