I currently use an iMac with the latest version of El Capitan which has updated the Printer Driver (Canon Pro 9500 Mk 2) to 18.104.22.168. It now ignores my print Layout setting in Lightroom. I regularly print an art image on A3 German Etching Paper through the front tray. My cell height 32.00cm, width 25.00cm, margins Left/right 0.34 cm and Top/Bottom 3.50cm. this has always centred the image on the page. I have this as a preset which has worked for several iteration of Windows/Lightroom. I acquired my Mac late last year and it worked fine until yesterday when the output now prints Leaving a margin of 0.19cm at the bottom and 0.08cm on the right side instead of centering the image. Any help would be most appreciated.
I've found that Apple's printer updates can cause far more harm than good. Not sure if this will help, but go to Canon's site and download their driver there and reinstall it.