The "flapping" makes me think that they might be a defective batch of shingles, and they aren't sealing together. Can you easily lift the shingles? You shouldn't be able to, if they're properly sealed.

If the shingles lift in the wind the lower edge of the shingle above could be causing it to wear the granules of the shingle below.

If you know the manufacturer, you can have a rep. come out to take a look.