It's not hard at all. Download IFOEdit here: http://www.videohelp.com/tools/IfoEdit
Just open VTS_01_0.IFO and under VTS_PGCITI select your PGC (there will probably be only one). Then in the lower window you can scroll down until you see color values like shown in my screenshot. Just change the out of bounds values and save the IFO file.
If you use DVDSubEdit, I think another way to make this work is to open your DVD (using “Open full domain”) and then click on one of the colors next to 'b,' 'p,' 'e1,' or 'e2.' Now you'll see this:
Like it says, Shift-Click on the colors that look black or white and chose to set them to black or white again. Then once you "Save all changes" it should repair the incorrect colors.