You don't need opposite sexes. I've played through the game a few times, and I always use the same pair of chocobos to get both my green and blue chocobos. I'd say you just have bad luck.

Best thing to do is get your Carob Nut ready, save outside the ranch, then continually breed and soft reset until you get the choco you need. It might just take a while before you get the right sex of the right color. I know I've had to soft reset over a dozen times before.