Every time you reset your drivers/update your print preferences, it makes sense that all the application-specific print settings would reset. Every time it updates the preference file, it re-saves over it and the base preference file wouldn't carry any data on how many copies to print in each app.
I'm not a Windows person, so bear with me. Do you HAVE to setup the print drivers Every time you want to print something? On Mac, you set them up once and you don't have to reopen them to get extra options from the CS applications because the application itself opens the driver. I assumed it would be the same on PC, since it would be a pain to have to reinstall the printer every time you wanted to print something.
I'm having the same issue with all my PC's in deployment (over 5) running InDesign 5.5. Does anyone know if this goes back to the old (Windows XP) way in CS6? I'm assuming not since this has more to do with the OS (Windows 7).
FWIW, I never print from InDesign. Printing is not really its strong suit.
Best to export a PDF and print that.