So, if I understand right, you mashed your grain, drained the tun, then added more water, then drained the tun again to get your second 5 gallons. You boiled the two runnings separately to make two beers, and the second was darker than the first.
That is odd, usually the first runnings will be darker than the second runnings.
Out of curiosity, did you take the OG of the second beer?
Did you remember to boil and hop the second beer?