Are you using composite video for sync? This can cause interference in your image like you describe. Use composite sync with a buffer instead, it should help. A nice shielded cable is good too.
I have connected the Neo using bnc male to scart female cable that I bought from someone making them in UK. I had an RGB cable without shield but then I bought another with shield. No difference.
If I use just composite there are no interferences. In RGB there is the problem.
My jpn N64 connected with S-video has also a slight interference problem.
My pal megadrive RGB, pal Gamecube RGB, pal wii component, pal Xbox 360 component, have a clear perfect image.
What is "composite sync with a buffer". I think this might be the key for my problem. I have lots of AES games that look shitty...I can't get a 100% satisfaction from my NEO
I also aquired a super famicom with RGB cable but had no time to check it out...