What temperature did you store the second carboy at? The banana flavor could be the yeast reacting to warmer temperatures. It's odd the second half was sweeter though, I would have thought the fermentable sugars would have been consumed in the primary, so both should have the same sweetness. How long were you in the primary before transfering? Did you take a gravity reading? I'm probably reaching here, but maybe you transfered before the beer completely fermented out and one secondary got enough yeast to finish the job (likely the one racked near the yeast cake on the bottom of the primary), and the other one didn't.