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Ok. If you are powering the Arduino via power jack VIN will output a high V. Yry using a multimeter on VIN when using a power jack vs USB and note the difference in voltage. Anyway, when powered by the power jack, instead of using VIN try using the 3.3V and see if that helps.
Try using a resistor in series with the LED or a different color LED. Most likely the power from the Arduino is over powering the LED