Are you importing all of the PDF’s into MAPublisher at the same time using the Multiple Data Import tool? Are the files referenced using the same coordinate system?
Personally, I would export them individually from MAPublisher as GeoTiffs and mosaic them together in Geographic Imager if you have access to the software. If the files do not line up with each other properly, it would also be easier to correct the georeferencing in this software.
I would suggest contacting us through help.avenza.com so that we can take a look at your workflow in more detail.