kze you are correct. we have a water conditioner because we have very rusty water. while it keeps all my appliances and clothing from turning brown and rusty, i think because the water sits in the toilet, it starts to build up a little. the only product that completely gets rid of rust is a product called WHINK...it comes in a brown bottle and has kept my toilets gleaming white. i have tried it all...the stains laugh at CLR, barkeepers friend is too gentle on REAL rust, and bleach makes it worse. WHINK is hydrochloric acid so you cannot mix it with anything!!! just squeeze it in the toilet, scrub it around and leave it. if the stains are bad, it will take several treatments. i squirt it weekly and even though it says do not use on color toilets, i have done that with no problem. i have the "bisque" color toilets and one white but it does just fine.
i can only find it at ACE hardware, but you can also by it online. hope it works for you!