Arduino uno strange happenings

Has anybody else had this problem. I was using the fade program to test a single LED. I hooked up the led from pin 9 though ground and nothing happens. When the resistor is moved to the 5 volt it works. Any idea on why this seems to be active low. I have tried two different boards same result. Please help.

The LED has a positive and negative side.

Where was it before?

With the LED from pin 9 to GND you may have killed the pin output driver (high side), turning the output into open collector. If the resistor now sources current from Vcc to pin 9 and LED the remaining transistor can short-circuit the LED and thus turn it off.