These stains, especially if they are brown/rust looking and are streaking down from the toilet bowl rim are caused by hard water, ie calcium and mineral deposits. I thoroughly cleaned them off with CLR, took a lot of sdraping with a plastic scraper. Then what i did was to put 3 Overnight Polident denture cleaner IN THE TANK, and leave it in overnight, when the toilet won't be flushed for several hours. If you see the stains reappear, put in 3 tablets for 3 to 4 nights in a row.