I went back through and re-edited this correctly, and I'm quite happy with the result. Problem is, when I render the final cut, there is one (that I can find so far) scene, right before a cut that repeats 2 or 3 frames, then goes to the cut. It's very obvious, and I can't figure out how to fix it. I've cut frames out of both sides of the cut and re-rendered it several times, all with the same result.

At this point should I render the whole thing, demux it again, dump it into womble and try to cut the frames out again?