We had rust stains (mineral deposit?) in our toilet bowls that simply wouldn't come out with any of the liquid "Works" type cleaners. My wife finally found a pumice-stone-on-a-stick product in an Old Vermont catalog.

I expected it to be another loser, but it worked great! You can really rub off the stains without too much work, and apply your energy to the specific offending portion.

I've since found them on the shelf in our local supermarket, near the usual cleaning products. They look like a big gayish stone popsicle on a stick. It might be worth a try.