Is it per chance one of the Sanagloss models?
Post #19 under the POLL thread in toilets describes a problem with an unremovable yellow stain at the water line of a Sanagloss toilet. There has been no answer suggesting a resolution of the problem.
If yours is also a Sanagloss model, it probably supports a hypothesis that there could be something about the Sanagloss finish that makes it susceptible to something in some water supplies. It may be smooth but if it is not totally inert or if it is porous it could develop a permanent stain. Being smooth does not preclude microscopic porosity.
If I were manufacturing these things I would get one of my agents to replace the toilet and send it back to me for analysis, unless I already knew what the problem was. I suspect that someone with a scanning electron microscope or some of the other high tech analytical systems could determine what the elements of the stain are and why it is occurring.