Sketch not starting (sometimes)

I have an issue with one of the Arduino Nano Every. This was reproduced only on one board, but I am curious what could cause this behavior.

Board is powered via VIN pin (12V DC adapter). USB 5V power is disabled on hardware level - I have taken the diode off to prevent it entirely, because board can be used only via external power supply to power the stepper motor.

The problem that occurs quite often with one of the boards is that after power is connected, the sketch does not start (I have added LED blinking into setup() to confirm that). However, Nano is detected and COM port created, so I can connect via serial monitor (and get 'à' character on every connect). It usually happens if the board is left unpowerd for at least an hour or so. Once it starts, it works even if I cut the power for a few minutes. I can still flash it normally and if I do that, it starts normally after it is flashed.

So to me it looks like that ATSAMD11D14A holds the ATMega4809 in bootloader state or something like that. I have also tried resetting ATSAMD11D14A by connecting its D11 Reset pin to the GND. This resets ATSAMD11D14A successfully (Windows chime etc.), but the sketch still does not run.

I have also heated up the components on the board (in case there were any cold joints) but it did not help.

Additional info:
M_MCU hardware version: 1
M_MCU firmware version: 1.07
S_MCU hardware version: 1
S_MCU firmware version: 6.07