So for me the conclusion is:
If going into mencoder using a XVID where the mencoder internal ffmpeg Mpeg4 codec is used, your colorproblems have been solved.

BUT if you go via avisynth and makeAVIS into Mencoder then colors are wrong.

So the processes of the XVID will be as following:

The xvid source case ... going directly into mencoder
XVID direct Mencoder-Decoding Using ffmpeg Mpeg4 decoder Mencoder-Encoding to mpeg2 Colors ok!

The xvid source case ... going via avs/Makeavis into mencoder

XVID decoded via avisynth using XviDmpeg4 system decoder as the avs is converted to avi via makeavis that one will be then processed through ffvfw.dll in mencoder.

You see the difference?

- xvid directly going into mencoder only ONE decoding codec is used!

- xvid via makeavis TWO other codecs will be used! XvidMpeg4 and ffvfw.dll !

So it could be that ON YOUR SETUP (dont know if system or mencoder) theres a conflict between Xvidmpeg4(or ffdshowmeg4) and the mencoder encoder !?? BUT ffdshow uses libavcodec, so the result "should" be the same as directly decoding the XVID using mencoder.

Now Im lost, as I dont know what "really" is set up on your machine and what could be the guilty one which affects the colors on your machine, .. as I dont have these probs.
I told above which codecs I do use and maybe the case of an athlonXP in my case is maybe an essential reason???? I dont know?
But threads like this should clearify that even if it takes a long time