The xScaleFactor and yScaleFactor were moved out of the INI file and into the Tools : Options dialog (on the Miscellaneous tab). These were designed for minor dimensional changes to compensate for scaling changes in some printer drivers. For example, if a line that supposed to be 8 inches long printed as 7.95 inches, you could use the ScaleFactor to correct the printing problem.
Starting in Origin 6.1, you can set the Page dimensions (under Format : Page) and not have these reset by the Printer (when you look at Print Preview or try to Print) if you uncheck the Width and Height check boxes in 'Use Printer default dimensions when printing'.
For any other Origin version, the normal solution is to adjust the layer size so it appears on your page in the correct proportions.