I came across this question on electronics.stackexchange today. Olin Lathrop, whose opinion I have come to respect deeply over the course of many informative answers, posted this in his answer:
Now that you've posted the schematic, a straight answer is possible. That schematic is a sloppy mess, but I know that's not your fault. It doesn't say much about the folks that designed your arduino board though. Yucc. It makes you wonder what else they didn't pay much attention to.</blockquote>
Indeed, it makes you wonder. You don't need to wonder much, however, once you realize the failure in (and the subsequent repeated failure to correct) header placement.
Seriously, guys, are .1" centers that complex, really?