If you're having trouble flashing the ArduPilot code with Arduino 13, try upgrading the bootloader on ArduPilot to the latest version. You can do it with your AVR programmer in the Arduino IDE or use AVR Studio to program the board with the ATmegaBOOT_168_diecimila.hex file found in the Arduino folder hardware/bootloaders.
I was having that problem and this fixed it for me.
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