Questions:

1. Does it take 5 seconds for the LED to come on or does the LED stay on for 5 seconds.

2. Have you tried not using serial input to turn on the LED. Not just make it blink like Skimask had you do, but re-write so when PIN? is high LED on. (simple switch )

I am getting at, if the above #2 works fine you may want to look at the signal duty cycle coming in from the serial.