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I believe this is the same as the well-known misalignment of SRTM data, for example, see the osm2garmin documentation (search for "SRTM contour shift correction").  I've never seen any real explanation of it, though, just speculation.

It's more or less standard when generating contours with Srtm2Osm to use something like " -corrxy 0.0005 0.0005", though my understanding is that the amount of error depends on the location.

-Mack