@ CC, are you refering to playing double pedal ? I believe it has got something to do with one leg being stronger than the other.
I used to have the same problem as you, furthermore, I also experienced having the right leg sounding louder than the left. Thus I kind of incorporate exercises that will put more work on the left leg, ie. leading the with the left or incorporating rudiments into exercises.
Doing rudiments on the legs in fact help alot in building control in my opinion, if you legs can do rudiments comfortably, it shouldn't have any problems doing straight 16s notes.