Always a joy with this level of helpful support! I guessed as much with the .ai being a secret jungle of proprietary code. And yes - the pdf is not centered. However, I cannot see the "center on page" option when exporting the pdf. This is what I have - using MOI3d version 3...

Hmm... I cannot seem to attach pictures on here for some reason

Also, there seems to be no options for setting the output pdf page size