You may have over loaded/shorted the 3.3V supply mistaking it for the 5V supply. The 3.3V supply is very low current and is provided by the Serial-USB bridge chip (FTDI).
See if you can get 3.3V from the board (using a meter maybe?). If not, you may have blown the FTDI chip on the board. They are not expensive and I have personally removed and replaced them (though its certainly one the HARDEST things you might want do if you manually repaired a duemillenove.)
Good luck.