Hello Michu,
I tried exactly the same thing with my Arduino Duemilanove (368 based) and Rainbowduino v2 (same chip) with no luck (it was the very reason that lead me to study the Arduino bootloader process, in fact). What I can tell is that in theory your setup with identical chips should not work, since they share the same bootloader. One possibility is that one of the two boards uses the old 19200 baud bootloader, while the other has the new running at 57600 - the Arduino IDE is smart enough to notice when programming the board, and you won’t even know it.
For your reference:
- http://www.arduino.cc/en/Main/Bootloader
- the file arduino-002X/hardware/arduino/boards.txt
- the file arduino-002X/hardware/tools/avrdude.conf
It passes the reset signal on to the connected board; but the signal also arrives to the Arduino IC (as you can see from the L led flashing).
Antonio