The AMV that I made a nice MPEG-2 out of is YV12 and was encoded directly, no AVS file involved. I've tried encoding my own files with and without AVS scripts in both YV12 and RGB colorspaces. Same results every time.
For kicks I used that nifty Info command on both my original, uncompressed AMV file and my MPEG-2. All the values returned (that were not deliberately altered when the MPEG-2 was made) are exactly the same except for the video pitch...which has something to do with the fact that YV12 got involved in my MPEG-2 (I think). So I guess that doesn't help.
As an aside, the MPEG-2 is still utterly unreliable - during playback it looks terrible, but if I capture a frame it looks so close to the original footage that I actually have to hold them side by side to confirm there is a difference. And the difference is perfectly described as a "slightly warmer" color shift, which is what one person who wasn't aware there's a "problem" with my MPEG-2 said is all he noticed, insofar as my MP4 and my MPEG-2 not matching goes. Slightly warmer is fantastic, unfortunately it can also turn out broiled!!
No worries about trying to re-encode it then, I'm fine with a slightly warmer version. ^_^