I had the same problem.  They say you have to use QB checks.  I have them.  But the vendor checks and the payroll checks do not line up the same, even though using the same checks.  It's the software that is the problem.  They have it set on two different formats, instead of one that both vendor and payroll checks can use.  It's like printing a document that's single spaced (vendor cks) and double spaced (payroll cks) on a double spaced paper (with printed lines on it of course).  I couldn't get them to understand that.  I yelled and yelled and finally just gave up.  Makes me want to go back to QB Desktop, or a new bookkeeping software all together.