I would not have expected the power supply change to affect the situation.
> When D45 is ON, 4 is HIGH and 5 is LOW. So I don’t understand how D410 and D105 can both be on simultaneously. For D410 to be on, 4 is HIGH and 10 is LOW. But for D105 to be on, 10 needs to be HIGH and 5 is LOW.
That’s a slight oversimplification. D45 is a blue LED, which should have about 3.6 V across it. If line LED10 is not connected to anything, the situation is also described as having D410 and D105 connected in series from LED4 to LED5. Because the red LEDs light up with about 1.7 V, that can be enough voltage to light up those two LEDs.
Now, there is some subtlety to the design, and things usually work as intended. However, if even a single LED is damaged or a resistor isn’t connected properly, that can screw everything up quite well.
The next thing to check is (with power off) the resistance from each output pin of the microcontroller to the LED1-LED10 lines. Refer to the circuit diagram, and touch your probes to the “shoulder” of the microcontroller pin and to the end of vertical jumper atop the red ring.