The problem isn't with your codecs or anything, its the group's encoding. The new OP and ED are 30fps while the episode is 24fps. Shin-Otakus encoded in 29.97fps which makes their OP and ED smooth, but you may notice that the ep itself may stutter. Aone/ANBU did theirs in 24fps making the OP and ED stutter but the ep doesn't stutter. Because the OP and ED is 30fps and the Episode itself is 24fps, the only way to make it smooth is to convert it to 120fps since 120 is divisible by both 30 and 24. There is a way to do a pseudo-120fps encode with drop frames but I doubt the encoders know how to do it since they didn't do it back during episodes 26-54. So until Naruto gets a new OP and ED that is 24fps, it will always appear like it stutters.