returns do not match

I completed my return online but did not submit.  I then decided to purchase the Deluxe option from Costco (cheaper) which is through the PC download.  I completed them both and there is a $400 discrepancy with what they both say my federal return should be.  State return matches for both.  From what I can see it looks like the PC version is not adding my credits to the amount of taxes that I paid (the online version is doing this).  Anyone else experience this?