Yes old fuel does turn a darker color. It also smells like laquer thinner.
I would be concerned as it sound like you have some other problem as you state the fuel coming from the tank is ok but in the return line it is dark. You also have run a few tanks thru and the problem is still there. Usually after the second tank the problem will clear up. If you are saying the fuel coming from the tank is odd colored always then I would be concerned of the condition of the tank.