The FTDI based boards don't seem to run into this problem because it appears that they don't stream out serial data unless the port is accessed. On my Arduino Duemilanove, with the following code:
void setup() {
pinMode(13,OUTPUT);
Serial.begin(9600);
delay(100);
Serial.println("Here we go, duck.");
}
int count = 0;
void loop() {
digitalWrite( 13, HIGH );
Serial.print("*");
count++;
if ( count == 80 ) {
digitalWrite( 13, LOW );
Serial.println();
count = 0;
delay( 200 );
}
}
The LED blinks whenever the board has power, but the TX light only goes on when the port is accessed with the serial monitor, minicom, or "cat < /dev/ttyUSB0". The means that the FTDI based arduinos are not subject to this issue -- they're able to be reprogrammed easily, even if they contain a program that hammers the serial port. The Arduino Uno behaves differently in that the TX light is always on.