The first file will contain default settings if you change the "Job Options" in system-config-printer. The second will be used if you save options in a printing dialog of an application which is running as root. The third will be used if you save options in the printing dialog of an application running as yourself.
Jesse, can you check (and attach) the following files:
/etc/cups/ printers. conf
/etc/cups/lpoptions
~/.cups/lpoptions
The first file will contain default settings if you change the "Job Options" in system- config- printer. The second will be used if you save options in a printing dialog of an application which is running as root. The third will be used if you save options in the printing dialog of an application running as yourself.