Please see my comment above. I had the same issue, but was able to solve it by printing the pdfs from the Chrome browser. It's not exactly fun, but you can use a combination of custom scale in the print dialog, and the vertical and horizontal alignment adjustments within quickbooks. It took me about 8-10 tests to decide on a final adjustment, but all entries were within the W-2 boxes. Maybe this would work for you, too.
