I see that this guy Hexy the Hexapod robot controller
had problems when trying to provide 5V at the barrel jack. He then switched to the Vin. This tells me that the 12V at barrel jack is being dropped on the chip at some point.
ok after reading this manual http://wearcam.org/ece516/ArduinoLinux_by_ManoelCarlosRamon_9781430268390.pdf
on page 42 lists some of the highlights between gen1 and gen2.
The power regulator now supports voltage between 7-15V DC.
So, there you have it. Gen1 strictly requires that 5v barrel jack input, whereas the Gen2 handles 7-15V.