Printing from FileMaker is dictiated by the printer and print driver that is installed on that machine. You can switch printers and see in preview mode how much difference there is (sometimes quite a lot).
The default printer being used on the desktop is probably way different in size than what the FMGo clients are using. Assuming you are scripting the print process, you can use a page setup step so the desktop will "remember" the page orientation and printer selection.
Hope that helps