flashing rusting. Flashing should be of galv material and not rust.
If you have tried clr with no positive results, I would guess that you have tried the best. Too much rubbing and cleaning could compromise the shingles.
If the flashing is causing this then I would attack the flashing now. You really cannot remove it either so, I would sand it wire brush it then prime it with rustoleum primer then paint them and maintain them until next roof repair.
I have seen grit comp asphalt shingles actually show running rust on their own. It has been noted that some of the grit could contain small portions of iron that will cause rust runs on their own. Within warranty and with receipt of shingle purchase the shingles can be replaced, but labor is not included. Labor is almost more than material.
I would say that your problem cannot be readilly solved with out a replace. Do not get on the roof on hot sunny days, you will also comp the shingles.