Each successive scan of a MODIS Level 1B image appears to be shifted Westward due to the Earth’s rotation during the 1.48 seconds between each scan. This effect will be greatest near the equator (about 1km), and diminishes toward the poles.

To correct for this effect, you must use the geolocation data provided in MOD02*KM Science Data Sets "Latitude" and "Longitude" to map each pixel onto a Lat/Lon grid. One difficulty is that these coordinates are provided only to 1KM resolution for the 250m data product; if you want to map the full resolution, you must interpolate/extrapolate these coordinates to every pixel of each scan.