Do you have an example script that shows the problem?
If you are only getting the problem when running MPEG2 into AVISynth, then it can be fixed with colormatrix.
Just add the line colormatrix() before the ConvertToYUY2() line.
You can get the plugin here.
http://www.geocities.com/wilbertdijkhof/ColorMatrix_v19.zip
edit:
BTW, if coming from an interlaced source then you would have to unfold the fields, then colormatrix the results then fold them back again.
-L