I've noticed that the Serial Port stops transmitting a few seconds after a PC based terminal/communications program is closed (TX LED stops blinking). However, the Arduino software continues to execute (I blink the pin 13 LED periodically), As soon as the terminal/communications program starts again, serial output begins again as evidenced by the TX LED blinking and serial data being displayed.
The Arduino code is not setup to receive serial data.
What is the problem? Opening and closing the serial port resets the Arduino. When the Arduino starts up, and finds nothing to connect to, on the other end of the serial port, is doesn't actually send data. The ATMega328 chip does not manipulate the LEDs. The other chip, the Serial to USB converter, does.