I would bet you have hard water with a high ph or they are eating massive amounts of a pigment called melanin. read this, might help you. Great overview of color, pigmentation, and how water quality aqffects color. There is a reason the japanese use soft water with low tds and low ph. That reason is called red.
http://www.koimag.com/features/artic...rs_of_koi.html
Also newsflash, their water out of the tap isn't a whole lot different from ours. If you have hard water with high ph, I can help you fix that for relatively cheap. By cheap I mean less than $200.