i have had several engines over the years that had the "factory fill" coolant turn a nasty "poop" color, and it took several flushes over a couple month time period to clean it up so it would remain a clean, green color.
also, i'm not a fan of the new style "pre mixed" stuff. some of that can turn color when mixed with any residual coolant left in the system.
GM dexcool is the worst of the worst, and should be avoided at ALL costs !
as already been mentioned, use distilled water with a QUALITY coolant, but you may have to flush a couple of times to get it to stay clean.
i am also leaning toward a coolant filter plumbed into a radiator hose, but i haven't pulled the trigger on one yet.