I tried to upgrade my apu1d4 firmware to the latest release (v4.11.0.5).
After successful flashing through flashrom on the installed debian, the board only boots randomly about every 20 power cycles.
It seems to hang, with no output on the serial console for at least 30 minutes.
Once it boots, it does so without error and boots to OS. Rebooting from the OS works stable.

I tried to downgrade and get the same issue with versions v4.9.0.5 and v4.6.8.
If I downgrade to apu140405.rom (https://pcengines.ch/file/apu140405.zip on PC Engines APU1D4 page, the boot is successful every time.

Serial output directly after flashing + soft reboot:

SeaBIOS (version rel-1.12.1.3-0-g300e8b7)

Press F10 key now for boot menu

Select boot device:

1. Payload [setup]
2. Payload [memtest]

I then powered off and cleared CMOS.
Then, in this case, two power cycles later, next success 5 more cycles:

SeaBIOS (version rel-1.12.1.3-0-g300e8b7)

Press F10 key now for boot menu

Select boot device:

1. AHCI/0: KINGSTON RBU-SMS100S360GD ATA-8 Hard-Disk (57241 MiBytes)
2. Payload [setup]
3. Payload [memtest]

When unsuccessful, no output at all, blank console.