Didn't you know that the NPN transistor inverts the logic? Without the transistor, the LEDs light dimly when the output of the microcontroller goes low. With the transistor, the LEDs light brightly when the output of the microcontroller goes high.
To have the same logic as before, you could drive the anodes of the LEDs from a PNP transistor then the cathodes of the LEDs are connected to ground. Then the LEDs will light brightly when the output of the micro controller goes low.