that sounds more like a system config or system driver issue, and not FFXI.

Some of those Realtek solutions allow you to customize some of the jacks. When it is set in different speaker modes (2.1, 4.1, 5.1, etc) at least one of the jacks usually changes it's role and such. In many of their solutions, one is a sort of "versa-jack" and can be set to run as line out, speaker out, digital out, etc. You may need to go through your Realtek control panel to see which one the headphones have been assigned to to make sure you are plugging into the right jack.