BJT not switching (off) fast enough?
You will get confusing results if you measure Vce because the pullup is nonlinear (due to the LED). Try measuring the voltage across the 470 ohm resistor. Or parallel the LED with 1K and go back and measure Vce again. 

I suspect your problem has nothing to do with the transistor and more to do with resetting the micro due to poor bypassing or something of that ilk.