Solution: (from http://www.arduino.cc/cgi-bin/yabb2/YaBB.pl?num=1201441300): it seems to be a problem w/ the linux driver. Just insert "stty -F $(PORT) hupcl" right before the avrdude command (where PORT = the usb device such as "/dev/ttyUSB0"). E.g. in the Makefil:
You may also have to set your baud rate to 57600 (at least for the 328p).
stty -F $(PORT) hupcl
$(AVRDUDE) $(AVRDUDE_FLAGS) $(AVRDUDE_WRITE_FLASH)
It's such a relief to not have to use their IDE! Point+click to edit was driving me nuts.
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