The component encoder inside the Omega was designed by shadowkn55 but the S-video/Composite encoder in the Omega is the same as in the Neo Geo AES, the CXA1145 so I don't know if anything can be done to fix it.
Are you playing in widescreen or 4:3?
Make sure the switch on the back is on component and not RGB.
Well ok, I'm an idiot apparently. Now the only problem is that I'm stuck with overscaning issues just like the ones of my first picture.
Time to look for a service manual, I guess