it makes more sense that this is a form of drm/file validation check that occurs.
the xbox goes through everything you have on the drive checking the drm rights or checksum validation on it. and possibly the more youve got the longer it takes. but itll still take time even if youve only got one thing as it grinds away working out if the md5 is correct for the file and the drm is correct.
auto defrag.... its not that. it wouldnt defrag all the time on the same single thing. if a drive is defragged on a pc and then you try and defrag again itll go through in a second. not take 45 seconds. even on a laptop itll be the same so its not because its only a 5400rpm drive used in 360's.
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