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Did you verify before doing anything else with the card? If you let the Kobo boot it, it's normal for differences to appear. Same if you try to resize partitions.
Otherwise it's very odd for there to be a difference in the first sector when supposedly nothing else touches the card.
Unless you're making a mistake like putting the image on /dev/sdx1 instead of /dev/sdx
Other than that I have no ideas... if you are located in Germany, I could send you an old 4GB card correctly preloaded with H2O image (and verified to boot in my own H2O, as in - the original H2O, not the later H2O2v12)
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