Well...I don't have a way to open the Eagle board file just now, so I can't see how the headers line up with a Duemilanove or a UNO or a Mega board, but regardless of the component designations on the various schematics, here's the deal**:**
There are two eight-pin headers on that Shield schematic.
Position 6 of J1 is clearly marked "PIN13" and position 7 is marked "GND" and position 8 is marked "AREF." Therefore, I infer that position 3 of J3 is "PIN2" and not "PIN10." Similarly, position 5 of J3 must be "PIN4" and not "PIN12."
In other words, J1 on the Shield plugs into J3 on the Duemilanove and J3 on the Shield plugs into J1 on the Duemilanove. (The same designations appear on the old Ethernet shield schematic, and I do have a couple of those, and I can verify that that's the way it is.)
Regards,
Dave