The problem is similar to this http://forums.adobe.com/message/4431235#4431235
Illustrator simply does not save any of the settings in the driver tabs (such as custom print sizes, paper tipe, source tray etc) unless I hit the Print button (e.g. I cant save those settings temporarily by pressing the Done button nor I can save a print presset for a later use), and that is a very very very annoying thing an it brings back some memories of the time I upgraded to CS and CS2 and the case then was even worse because it didnt save the printer driver settings even by printing and allways reverted to the default settings, and now I remember why I hate Adobe so much, because they never had a fix for that until CS3 came out.
That issue has been tested with XP 7 Vista both 32 and 64 (a lot of printer drivers) and it is not a single configuration problem, so please before asking some questions about the kind of the system and software etc do the following with your CS6 (or CS,CS2) and please tell me what happens. Choose File->Print and in the dialog choose whatever printer you have, press 'Setup...' button in the lower left corner, ignore the stupid prompt that some unknown Adobe genius tech invented, press Preferences button in the new Print window that pops up and in the printer driver UI window choose whatever setting you like that differs from the default setting, and then press Ok then Print and in the main Illustrator print dialog pres Done (but not Print if you are in CS6) button to close the dialog. Then open the Print dialog window again, navigate to the printer driver you just adjusted and please tell me what settings you have - those that you adjusted or the default settings. Thank you in advance!
Thank you for the responceq Johny_07, unfortunately it solves the problem only if I have to specify the size of the media, but I need to specify the source tray, paper type and so on, parameters that are not present in the dialog box, and those are not remembered by Illustrator also. Do you experience that problem, I have allways wondered why there is no info concerning that problem, is it happening only with my instalations or it is a general program bug.
I have the same problem, but I need a custom paper size and that option is grayed out on the Media Size drop down menu. I am a Mac OSX user printing to a Primera LX810 label printer using Illustrator CS5...