“My roof is streaked with black stains. Is there anything I can do to get rid of them? The shingle manufacturer says that staining isn’t covered by the warranty because it doesn’t affect the performance of the shingles.”
The staining may be attributed to mildew formations and can sometimes be removed with pressure washing. Be warned however, high pressure washing will likely will remove some of the mineral granules used as a protective surface for your shingles. Even with wash removal, you are dealing with the symptoms of the problem and not the cause. Unless you can find a way to change the causative factors, the staining will likely return some time after the washing.
Some shingles are “mildew resistant”; they have tiny metal granules embedded along with the other mineral granules on the surface of the shingles which prevent mildew growth. As you drive around and look at various roofing systems, you will likely notice some roofs which have lighter colored shingles beneath metal flashing areas. The metal ions, which periodically wash off the flashing pieces, prevent mildew formations on the shingles.
In some cases, you will see long horizontal strips of metal installed under shingle tabs. The expectation here is for rain water washing down the roof to pass over those pieces of metal and thereby prevent mildew growth on lower shingles. This is something you might consider as a retrofit once you have removed the existing stains. If you choose this approach, consider installing several courses of metal on the roof surface to enhance its effectiveness. You might choose to do this only on the roof surface, which is most visible as a money saving measure.