It could be one of several things, but try to narrow it down to the cable, the port, or the GPU. First try to change out the cables that connect it to the TV. See if you can borrow another cable to see if your cable is causing the issue, from a friend or a local retro game store. If that doesn't work, then try to change the cable type. If you're using component then switch to composite. At this point you should also be changing the output settings (480i, 480p) for any noticeable change.
- GPU problems tend to show up as 'green spots' or 'speckling' in the picture.
- Issues with the AV port show up with Component output with the loss of a certain color. Red always seems to go first.
If its none of these, then you may have to go to more drastic measures. Hope this helps. :-)
After consulting some friends, the consensus is that your GPU has bad sectors resulting in it not being able to output those lines of video. Either you can live with it, or replace the motherboard. Sorry :(