I don't see how that's possible. Are you sure that the increase in balance due was not simply due to the amount in box 4 of the W-2 not being sufficient to cover the tax liability being added by the amount in box 1?
Try going back and seeing if changing the code E amount to $0 decreases your balance due. If it does, compare your Form 1040 with and without the actual code E amount to see what is being affected.
