PDF Alignment issues when upgrading from fop-0.95 to fop-2.3

I'm new to the XSLT FO world and came across an issue. I have my XSLT that
works well with the fop-0.95 processor and generates the PDF, but after I
upgraded to fop-2.3, it left my first page blank and started the PDF body
from the second page (my PDF has a header that appears fine on the first
page).

I figured out where the issue was, and it was because I had the margin-top
value set to 3 inches in the "fo:region-body" tag within the
"fo:layout-master-set" (please see screenshot). I had to change the 
margin-top from 3 inches to 2.5 inches for the body of my PDF to appear like
it was while using fop-0.95.

Does anyone know why this is happening?
I have multiple PDFs with the same layout, so if I need to upgrade to
fop-2.3 do I have to make this change to all of my PDFs? Any help is greatly
appreciated. Thank you.

<http://apache-fop.1065347.n5.nabble.com/file/t2984/XSLT_Screenshot.png> 



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