If you have identified the origin, then remove or replace that culprit now. Check the guy wires anchoring the antennae to the roof, make sure the eye bolts or what ever was used is made of zinc or galv material.
Some comp shingles have been made with minerals in them that with age will rust and show running rust stains. This is an internal flaw and if you have your paper work on the roofing, you might want to contact the manu of the roofing material.
Then as J or Henry has stated before, remove all branches or overhangs that cause moisture to remain on your roof. make sure the roof is ventilated properly so it does dry out.
In sum to your question, if you have used a pw and no results, you just might have to live with the stains. But you can stop them though.