Keep brightness high whilst multiplexing [SOLVED]
I don't see a schematic. 3 x 3 LEDs is 9 LEDs. 

If you are running the LEDs at 33% duty cycle (3 of 9 at once) then you need to pass 3x the current for the same brightness as DC (approximately). 

So if 220 ohms looks okay to you, then more like 68 ohms (the LED forward voltage will rise a bit). That may be enough to damage the LED if the multiplexing stops. 

That means that the LED is actually a bit less efficient if you are multiplexing it. The reason to multiplex is to reduce the number of drivers and port pins. If you want to be able to run 9 LEDs at 15mA average current then you need 130mA total. There is no free lunch.