It's a stupid question, but where are you applying 12 V? Hopefully, on the terminals marked MAIN-PWR. Check that the polyfuse next to those terminals is good. Also, with power on, check that you have whatever voltage you're applying present on the PWR header (next to the HE0 screw terminal).
Check that you have 5 V and 12 V on the headers between the ATmega16U2 and the ATmega2560. (12 V may actually be less or not present at all -- it's the output of a regulator supplied from MAIN-PWR, so it may not kick in properly until that's a few volts above 12 V. That's not a problem, because only HE2, FAN0 and FAN1 are supplied from that, and you can always flip the jumpers to supply them from MAIN-PWR instead of the on-board 12 V.)
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