Even so, I'm wondering what might be causing it and how I could avoid it. I'd like to eliminate any problems like this, particularly for contest submissions.
Here's a screenshot of the problem during one of the many slow fades in my video. The effect is especially noticeable in her skin and collar in this shot.

Also, here's my script:
I also tried exporting another version without mftoon because I thought that might be the culprit, but it didn't make a difference with this particular side effect.
AVISource("F:\Sean\Myvideos\Saikanogoodbye\final\GoodbyeBpreview8b.avi")
ConvertToYV12()
deen("a3d",4)
temporalcleaner()
mftoon()
Tweak(sat=1.2)
ColorYUV(gain_u=15)
Crop(8, 8, -8, -8)
LanczosResize(720, 480)
Thanks in advance to anyone who lends their input.