What happens when you print a layout from Prism 6 Windows, and the printer page size is different than Prism expects?
Prism 6 Windows always creates new graph and layout pages to the US standard (8.5 by 11 inches). When you print, Prism adjusts the layout page to match the page size of the selected printer and this sometimes causes unexpected changes in alignment.
Easy workaround: After creating a layout, but before spending much time polishing it, drop the File menu in Prism and choose Printer Setup. Make any changes needed (probably no changes) and OK. Now Prism will make the size of the layout page match your chosen printer, and won't change that page size when you print.
(Prism Mac gets the page and margin size from the printer driver, so this problem doesn't occur.)