@deanhowell
You have not added sample data alas (or luckily.;)
But i can guess..
PDF Pageformatter has the annoying flaw of centering everything.
So every port wil be individualey centered in it's defined pageframe.
So assuming the pdf you post is centered, the total extent is larger than the visibly drawn objects.
Stated differently, the center is not the center of the black bounded box.
To fill it out to the black border, you need to make the objects send to the port the only objects. That is, select the black bordered extent and nothing else outide it before sending it to the formatter.
Safe is seriously overdue on fixing that. ( i find this strange as you can simply calculate it)