The majority of peppers i can are either green or yellow. Red ones i save for salsa hot sauces, pickles or 1 to jar of peppers for heat. Tumeric is your friend when canning yellow or green peppers and pickles. Always have good results. As SL said when canning you will always have some color loss but it should be extreme. I would guess that you are not packing enough peppers in your jars before processing or like SL said u are overprocessing. Are your processed jars 3/4 or more full with peppers and have about 1/4 room of brine? If so fill your jars fuller this will help too. If your really concerned with appearance, process colors separatly and add a few drops food coloring to each jar before adding lids. here is a jar of wax peppers with jalapeno. Added a pinch of tumeric to jar before capping. Without it...yellow peppers will turn white when processed. Have fun, Good luck