I've had this machine awhile. Decided to clean it up, straighten out wiring and such. Basically tear down and re-assemble. One problem I've had the whole time and I hoped may have been solved was when I issue or any other shutdown command the machine acts as if it received a reboot instead. When it doesn't shut down properly the main nic seems to be dead when it comes back up. Driving me nuts. I don't reboot often but it's just an irritation that I can't solve.

I just looked into jumpers, I've reset the bios / cmos, added a fresh battery, blew out the dust, the works. I'd say it's quite beautiful inside the case (compared to before). I just can't figure this out. As I've recently moved the machine to a remote location on my land it's more of an issue. If I do need to reboot (updates or whatever) I have to manually go out and hard power it off, wait a minute. Then power it up in order for the network to come up. This has been an issue in both Ubuntu & Debian. OMV also showed it. I'm fairly sure that this is not a linux issue, rather a hardware issue. I just don't know what to look for. I don't think it's the mobo nic because it works flawlessly the rest of the time. Just after a poweroff cycle it's dead.

Any ideas?

Is there a BIOS upgrade for this thing?

I did do the most recent bios for the board. I can say that I did solve part of this. The network issue, or lack of it coming up occasionally has gone away now that I've realized that Linux doesn't need to know about the ipmi port. That seemed to get it hung up on boot. Removing all references to it in netplan or /etc/network/interfaces has solved that part. Now it comes up every time. Still doesn't seem to shutdown though. At least the network issue is fixed for the time being though.

First, try a (newer) PPA and/or vanilla kernel. If no change I'd try booting a live Linux, or maybe more than one, that is not a Debian or one of its derivatives. If you're running a DE on it, especially if GDM or Gnome is involved, I'd try different ones. If your NIC is an expansion card, try a different slot, or different NIC.