I have successfully flashed the seeeduino 328 with avrdude and ubuntu 9.04, so it can be done.
Don’t know if this will help you or not.
Two things for me are very different from your approach:
- I used adafruit.com USBtinyISP as the programmer, so mine read: avrdude -c usbtiny (etc.)
- I used the avrdude v5.5 but copied the section for ATMEGA328 from the seeeduino avrdude.conf file to the avrdude v5.5 avrdude.conf file. I copied this in right before the ATTINY2313 section in the conf file.
My guess is avrdude doesn’t like the type definition.