Neo Geo AES 3-6 S-Video sync issues

So I did a S-video mod to my Neo rev 3-6 and while the picture is crystal clear. Ive noticed some wavy lines that occasionally appear on screen. It looks like some kind of sync issue. I tried it out on different CRT's and seen the same thing. Anyone know of a way to adjust the sync or fix the issue. Everything else is perfect. Also I re capped the whole board and still see the same thing. Here is a short clip of it happening. Look at the "SNK" initials of the 3rd top score. https://youtu.be/Ps9SqiafceA
It happens on this screen at the top too but it's off camera in the video. Other screens have the same issue.

Ok so i tried a couple things today and found something very odd. I completely removed my S-Video mod and hooked it up with the stock A/V cable. To my surprise it did the same thing! So is there something wrong with my CXA1145 encoder? What else can cause this?