Like I’ve said before, I don’t consider Squeeze as a professional level application and the lack of decent colour correction tools is another reason why it isn’t.
That said, there is no reason that VP6 will be knocking out your chroma levels to a serious level unless you are aiming at a very low bitrate.
Try downloading a demo of Flix from On2 and see if the same thing happens with your chroma levels.
If you are serious about compression, I’d seriously consider looking at getting another application to do the job for you.
Are you sure your animation is YUV? What method did you use to export it from AE?