Electrical – Where do the RGB LED matrix resistors go

The problem ended up being a PWM issue. (It was solved in the comments, however I've posted the following to help future readers of this.)

First switch the Red or Blue with the Green. This will determine where the problem lies. If the Red or Blue still doesn't work then the problem is with the LED (very unlikely) or somewhere in the connection. Otherwise it is a software problem, like incorrect use of PWM.

Helpful links:

• Basics of PWM with an Arduino
• PWM with Arduino Video
• A much more advanced app note from Atmel about PWM

Without a schematic, based on your question, you have Common Cathode Led with TIP120 transistors? I assume you have them connected backwards from normal.

^{simulate this circuit – Schematic created using CircuitLab}

The TIP120 is a NPN darlington pair transistor. It normally expects to be on the low side of the load. You are using them for High Side Switching, which won't work. If your led was common anode, you could swap them around, and it would work (WITH THE RESISTORS).

But in this case, you have 1) A different signal level from the led power level (3.3v vs 5v) so Direct PNP transistor won't work, and 2) The Raspberry PI GPIO cannot source a lot of current. 16mA at max. So You need both NPN and PNP transistors. Some 2n3904 and 2n3906 Common npn and pnp transistors, but any similar would work

^{simulate this circuit}

I only show the blueled (5v source voltage - 3.2v forward voltage - 0.2v VCE drop / 20mA = 80Ω), do the same for the green led, and use a 140Ω or higher resistor for the red led.