I honestly don’t know what’s causing the issue you’re seeing but it’s not any kind of fault in the board design.
All the VCC pins are tied together and directly connected to the VCC pad on the edge of the board. There’s no other components or fuses between the VCC pad and the chip so if it’s working over USB, it would have to work when you apply power to VCC since USB ties in further upstream.
A simplified diagram showing how power routes through the board is below. As you can see, the VCC pad is directly tied into the ATmega chip and is closest to the chip. You have to go through the VCC pad when you power via USB.
