I called the support center and someone was able to help me work around the problem.

It had to do with the program my computer was using to print pdfs.

Download Adobe 11, then went to process my w2's.

Print the documents to your computer using Microsoft XPS document writer, which will allow you to save it as a pdf file, but as you are saving it change the type of file from OpenXPSdoc(.oxps) to XPSdoc(.xps).

Then open that document up on your computer and print it on a blank sheet of paper, hold it in front of the blank W2 form and see if it lines up.

This worked for us.