Are you aware that you can slice a small trace line on the Arduino PCB to disable auto-resets. I found it very useful for a couple of my projects.
Here is a clip taken from http://arduino.cc/en/Main/ArduinoBoardUno
The Uno contains a trace that can be cut to disable the auto-reset. The pads on either side of the trace can be soldered together to re-enable it. It's labeled "RESET-EN". You may also be able to disable the auto-reset by connecting a 110 ohm resistor from 5V to the reset line; see this forum thread (http://www.arduino.cc/cgi-bin/yabb2/YaBB.pl?num=1213719666/all) for details.