Applications can over-ride the driver.
Many applications just use the "last used settings" to make it more convenient for those who print lots of the same style.
The driver also has presets, that can be saved per app, so that may be the cause
MS Office uses last used setting no matter the defaults you set, so any change you make becomes the new default for that app.
Then there are server scenarios, you set the server via Printing preferences and usually it will populate those to the client, but if the server is 32bit and the client is 64 and vice versa, you need to set it in the Defaults as well on the server.
Then, it is possible that the printer itself is changing the settings via Bi-Di, but this tends to occur with the native driver and not the GPD.
Ok weird one that I seem to recall seeing a fix for but can't find it now. Xerox WorkCentre 7525. Using global print driver ps x64 5433.600.0.0. If I go to printer properties on devices and printers it is configured to print single sided and in color. However when I print from any application and select printer properties it is set to double sided. it will print single if I set it to print single there, from the application, but if I just hit print it defaults to double. I am unsure of where this is coming from since both the print preferences and default printer settings are set to single when looking at the printer in devices and printers.