First off, I love your avatar! It's the boy from bleach right? I'm still watching bleach on Hulu!
Anyways I've heard of muscle imbalances before. My right arm has harder biceps because I brush my teeth for so long. Lol
Even though you might be doing crunches, that use both sides at once the stronger side will compensate. Maybe someone could watch you or videotape you to see if one side is more elevated. If you do have a muscle imbalance you're going to half to target each side one at a time. For example side planks. Do each side for the same amount of time and reps. :) hope I helped