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I am little confused as well, the files on Altera/Intel website contains files for revision C, not D, as it marked on the PCB file, however PLX PCIe switch is on the top side and attached to the heatsink through thermoconductive resin, not like shown on the Altera's photo on the kit's Web page.
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Seems the retail photos are of an earlier revision than C. I've done a cursory comparison of my/our board and the retail photos, and aside from the U47 position, I only discovered a capacitor around the DC jack in a different position as well. But it all matches the revision C documentation.
All in all, I'd say it's pretty likely that the schematic has not changed in any significant way, from revision C to D.
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