On Linux, CUPS (or Common Unix Printing System) is used to identify and issue protocols to printers. There is nothing under Linux that actually pre-configures your printer or stores data on your printer. Each print-job is separate, and is preceded with configuration instructions consisting of those that are default settings or are manually set by the user. These settings may include, for example, the number of pages to print, or the number of copies to print, or even whether to submit the job using the duplex (two-sided) setting.
For your "mis-behaving" Linux distro, I would suggest the following:
1. Ensure you are using the proper print driver (as provided by CUPS) for your printer.
2. Check to see if you have properly configured the Print dialog so that your print-job is printed in duplex.
I know that with Firefox, the Page Setup tab of the Print dialog contains the setting for two-sided printing.
If you have verified items 1 and 2 above, and the problem still persists, then the issue could be a bug with the CUPS driver.
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