The wrong check number prints in Micr Line

We upgraded to Peoplesoft Enterprise application release 9.2 Tools 8.55.05 and converted the check form to BI Publisher.  The checks are printing, however, only the first check number in the sequence gets picked up in the Micr Line when the checks print.  I had to insert a Footer in the Check form in order to get the Micr Line to print properly.  I also had to insert our company logo's.  When I added the logo's I changed the location of a couple 'End If' statements and a 'End Group on the form which I believe is the reason the Micr