" Now my problem is the number is way below what my records show it should be."
That should not be the case. Since the compensation is calculated on a lot by lot basis you should be able to easily pick out a few instances of where TurboTax's number is too low. List out in complete detail all the elements of the grant and the sale. If your records are simply calculating compensation based on the discount that will almost certainly be wrong if you have Qualified Dispositions. The compensation on those sales typically is lower than the purchase discount and that might explain what you are seeing.
