Try powering the LED with an external power supply, I have a feeling it is bigger then the 5mm LED in your wiring diagram. What is happening I believe you are killing the 3V3 regulator, 3W is just under an amp, the regulator can supply about 150mA. Here is some tips to help:
Gil's Crispy Critter Rules, they apply to processor hardware:
Rule #1. A Power Supply the Arduino is NOT!
Rule #2. Never Connect Anything Inductive to an Arduino!
Rule #3 Don't connecting or disconnecting wires with power on.
Rule #4 Do not apply power to any pin unless you know what you are doing.
LaryD's Corollary's
Coro #1 when first starting out, add a 220R resistor in series with both Input and Output pins.
Coro #2 buy a DMM (Digital Multi-meter) to measure voltages, currents and resistance. Violating these rules tends to make crispy critters out of Arduinos.
Hint: It is best to keep the wires under 25cm/10" for good performance.