Rainbowduino v3.0 Led shine problem

I have to solve one problem with my LEDs, I have superflux RGB leds. These operates with 20mA, but rainbowduino cannot shine them. LED is definitely ok, cause when I power it via Rainbowduino 5V rail and resistor it shine. But when I compile simple example sketch and upload it to rainbowduino (in IDE I have set Arduino Duemilenove /w ATMega 328) leds do not shine. When I close look into LED I can see that chips are reacting (I can see turned on color chip on very low brightness)on compiled sketch sequence but cannot shine with full power. I measured voltage which came from used pins and it was approx 0.040V. Is there something like brightness which should be setup? I tried to power it via usb, and also via 9V adapter, result was same. I’m little desperate that I cannot find a problem. I’m using Rainbowduino Library v3.0 found on Wiki page

I forgot to mention that I still do not have finished whole LED matrix, should be my problem caused by this? at a moment I’m testing just with one LED connected to position 0,0 ? when I upload sketch which in loop change main RGB colors each 2 seconds on position [0,0] I found following cases:
When I have anode connected to VCC1 (pos0) and connect any R-G-B cathode to GND, led shine as it should. When I have connected all R-G-B cathodes to position 0 on corresponding pins and connect Anode to VCC 5V LED (5V marked pin on right) shine as it should and blinking as uploaded sketch says. But when I connect LED like it should be = Anode to VCC1 and each R-G-B to position 1 of corresponding pins it do not shine, I just see some indication that there is some sketch but no shine. I’m little bit deperate … any help?