What affects LED brightness?

To test if the LED are the issue or the drive, I would suggest you connect all the LED's with their 220 ohms directly to 5V power. If the LEDs are all the same brightness the its the drive, if the LED's vary in brightness then its the LED's

The other thing to note is Red and Green LED's have significantly different specifications due to the materials needed to create different colors. With the same 220 Ohm resistor the green will be much dimmer than the red (typically).