This has been a recurring problem with QuickBooks for at least the last decade that I remember and there is a fix that appears to work that is mentioned below using the Microsoft XPS Writer.  In any case, I'll go into a little detail as to how we resolved it as well.  First of all, it's highly recommended that you use blank perforated forms for W2 printing for Employees - it completely avoids having to deal with this issue, however, when you have to report your W2 Copy A to the SSA, you have to fix the alignment issue since it requires the use of the red ink official form.  Here goes:  First: Select the W2-Copy A 

Then use the Align button to generally align the top half of the form so that it prints correctly (the issue has always been the top half can be aligned but the bottom half fails to align properly)

Use the Print PDF to print the forms to any PDF writer (QuickBooks recommends Adobe, we use Nuance).  Once you have opened the PDF document then PRINT it again using the Microsoft XPS Writer using the .XPS format 

Then open the resulting .XPS document using your PDF writer

Before you print the resulting PDF document - set the ZOOM to NONE and UNCHECK the Auto-Rotate & Center boxes

Print your first page to test the alignment, both the TOP and BOTTOM should be aligned uniformly, if not, you can restart this process using the ALIGN as noted on Step 1, the difference now is that both the TOP and BOTTOM should be able to be aligned uniformly.

This has worked for us with virtually every release of QB and we are currently using QB Enterprise V 18

Happy Hunting