I would suspect that some software on your computer is periodically trying to open the serial port that it finds due to the arduino. Because of the auto-reset feature, this will cause the Arduino to reset, appearing as in otherwise inexplicable pause.
You can check for sure by something more noticable at the very beginning of your sketch (blinking the on-board LED a couple times rapidly, for instance.)
This wouldn't be completely unlikely behavior for cell phone or PDA sync software...