If you look at the schematics for the UNO and Duemilanove boards, they have circuits
so that power jack input and USB can co-exist without fatalities.
You're lucky you didn't fry the USB port on your PC. Last week I actually hooked up my
FTDI cable [same onboard I/F as shown here] to a board powered by the power jack, and
it shutdown my notebook. Luckily the USB port survived.
I discovered the idiots who designed the pcb had a TINY TINY 6-8 mil trace covered by
solder mask that was shorting across 2 pads that you wire together to power the board
from the FTDI header.
Who does something like that? Either you the user solders in a heavy jumper or not. Makes
zero sense to have a pre-existing invisible 6 mil trace bringing power in. How's about 50 mils,
guys!