My guess is that you might have some problems because of timer interrupts (or other interrupts?) messing up your timing. Just as an experiment, try adding this to the end of your setup():
cli(); // disable interrupts
Of course, this will mess up all kinds of stuff you might want to add later, like serial port I/O, use of timers, delay(), millis(), etc.
I say this because I was surprised when I tried generating radio frequency energy and encountered an unexpected tone modulated on top of what was supposed to be a pure carrier wave. See here:
http://www.arduino.cc/cgi-bin/yabb2/YaBB.pl?num=1166896036