Z390 Itx/ac - two flashing red light back of MOBO

Okay, first of all let me just say for the record that I don't own one of these Z390 boards so my answer will only be an educated guess. I didn't see a mad rush to respond to your question so I thought I'd give it a try, since I was just sitting here sipping an iced green tea at my favorite coffee shop, while listening to the wonderful Thelonious Monk playing in the background. :)

Your details were slightly vague since I see ASRock makes two Z390-Itx/ac boards, a Z390M-ITX/ac and a Z390 Phantom Gaming-ITX/ac, so it is a bit tough to know which one you actually own. It does appear that maybe you attempted to include a photo of your board, or of the two lights, but for some reason that photo must no longer be available.

Anyway, the Phantom Gaming has on-board Wifi and one Ethernet port, while the Z390M has on-board Wifi and two Ethernet ports. Performing a close-in zoom of photos made from both boards didn't seem to easily reveal the lights (actually LEDs) of which you wrote; neither did the pc board silk-screen that I could read provide any clues. Failing to find any definitive information about these mysterious lights it is now time for an educated guess.

Many desktop Ethernet ports will support a (bios) feature called Wake on LAN (WoL). When a "magic packet" is sent across the network addressed to a specific computer, and that specific computer has the WoL feature enable, the computer will power-on from either a sleep or power-off state.

To support the WoL feature the Ethernet port(s) must remain powered-on at all times to await the possible arrival of the "magic packet", even when the computer is powered-off. It is possible the two LEDs you see flashing when the computer is powered-off are simply representative of the on-board Ethernet port(s) that remain powered-on and serving their intended purpose in life.

Both Z390-ITX boards also have that on-board Wifi module. Just like the Ethernet port(s) and the WoL feature, the on-board Wifi module could support a similar feature called WoWLAN (Wake on Wireless LAN). Once again, if this feature were made available, it would require the on-board Wifi module to remain powered-on even when the computer is powered-off. So it is possible that one, or possibly both, flashing LEDs could be related to the on-board Wifi module.

Of course it is also possible that I am completely wrong and the flashing LEDs are some type of fancy LED animation feature that are popular with gaming motherboards. :)

By the way, as I was examining motherboard photos searching for LED clues, I was able to make the guess that when you wrote "bottom" you were referring to the side of the board closest to the PCIe slot. However, when you referred to the "back" of the board, I found that to be a bit more ambiguous. Would the back be the side with the rear panel I/O, or would it be the side of the board oriented deep inside the case, the side nearest to the memory slots? I'm guessing "back" meant the side with the rear panel I/O, adding some validation that my hunch that the flashing LEDs are related to the Ethernet ports and/or Wifi module.