amplifying the Rainbowduino

I think I can see the problem. I've just found the schematic for the Rainbowduino at http://www.trochotron.com/w/images/0/01/Rainbowduino_v2.0.pdf. Are your RGB row inputs the left hand inputs to the device marked RGB1 in that schematic, and are your column inputs the right hand inputs on that device? If so, it looks like the RGB row outputs of the Rainbowduino are active low, and the column outputs are active high.This is the opposite way round to the way your circuit is designed to work.

I can see two ways of fixing it:

  1. Swap the NPN transistors for PNP transistors and connect their emitters to +5v instead of ground. Likewise, swap the PNP transistors for NPN transistors and connect their emitters to ground instead of +5v. Also reverse the polarity of all the LEDs.

OR

  1. Leave the circuit as it is, but invert each row and column input using another transistor.