Could you be running into this?
http://code.google.com/p/arduino/issues/detail?id=661
I know I hit that problem and had to change ArduinoISP to use 9600 baud and the
programmers.txt file to tell the IDE to use 9600 baud, and then I was able to
program one Uno R3 with another one.
P.S. I didn't need to prevent the auto reset. Supposedly since optiboot 4.4,
the reset bypass is not necessary (and I had 4.4 on my R3).
Here's the thread where that tidbit shows up: