I thinking being too upright isn't the problem, but I've been wrong many times in my life. Can't hurt to try a different stem, especially if it puts you in a position more like you're used to. Is it possible that the longer top tube has you reaching farther forward than you should be?

Do you have the seat tilted down at the front, roughly level, or tilted up at the front? Strange as it may seem, keeping the seat level or even tipping it slightly up can help because it forces your weight back on your butt.