Stop cups, edit manually /etc/cups/printers.conf and add, for example:
in some printer, start cups
Go on http://localhost:631/ , Printers, set printer option, change something (or just click any set printer option without changing it), edit the conf again: settings are gone.
An other way to phrase it: using the webinterface overrides any manual setting.
These options should be supported by cups 1.3, according to http://www.cups.org/documentation.php/doc-1.4/ref-cupsd-conf.html and I can not use them, because if I insert them in the conf, and, later, make a change using web interface, I will have a conf breakage.
[URL] would suggest that you only use the web interface to set up a printer once...
There's nothing we can fix here, it's how CUPS works. If you want it to be changed you should file an upstream bugreport over at their bugtracker: