I’m not sure if it’s long-gop, but I don’t think that is the issue because I have many other shots that keyed just fine. It’s only when I enable the Matte Controls and render that the problem arises.
If you pick the NTSC DV Widescreen preset, it automatically changes the pixel Aspect ratio to D1/DV NTSC Widescreen (1.2). You can’t change that to square if you want the widescreen.