The only schematic is the one provided above. "Schematic (MAX7219 module)". The capacitors are 0.1uF 0805 and the resistors are 22K. I created a board layout from the provided schematic and then disconnected it from the schematic so I could repeat the layout 18 times and hand finish the final PCB layout.

I wasn't sure when I started this project whether the time taken to shift 512 x 3 bits into the shift registers at a speed fast enough to maintain persistence of vision via a single pin was achievable with an ATmega328. With that in mind, I split the channels so that if necessary I could shift the data through 3 pins simultaneously meaning only 512 bits needed to be shifted through each pin.

No I didn't have any problems. I guess you should check for shorts on the PCB or maybe the LEDs are faulty.