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This is not unexpected. The same issue exists with the MODIS filenames. Both MODIS and VIIRS L1 files are "chopped" into 5 (or 6) minute granules, but the scan rate for the sensors does not fall exactly on the 5 (or 6) minute boundaries. The L2 filenames are derived from the actual time of the first scan in the file. Sometimes this rounds to 1 second later than the nominal 5 (or 6) minute boundary.