Muxman isn't turning your subtitles red. .SUP files do not contain color information, just the subpicture images, so Muxman's default color palette is being used (which does not match up with your original colors).

You can use a program like DVDSubEdit (free) (http://download.videohelp.com/DVDSubEdit/) or DVDRemake Pro (pay but awesome) to correct the colors manually after authoring. (IfoEdit and PGCEdit might also work, but I've never tried.)

Now if you are muxing with Muxman and then using a program like VobBlanker to substitute your newly remuxed movie into the original full DVD, the original DVD's color scheme will take over and self correct your problem.