That's a really curious arrangement. Are all of the nails on the same row and in a continuous run of shingles? I've seen nails run off course due to operator error, but usually they realize it as soon as they put a shingle in on the row above.
I'm now starting to wonder if there's a problem with the sheathing and they were trying to keep the problem from telegraphing through the shingles.
Have you investigated up in the attic? What did you see?
R