This was alix1d embedded PC with FreeNAS running on it so my first thoughts went to file corruption. And I was right, there was some file corruption, but nothing that simple fsck could not solve. However, boot process still had issues.
I will not detail everything that I tried. It is sufficient to say that I wasted whole day playing with this thing. As last resort I decided to reinstall system.
As I went into BIOS to set my boot device, I noticed that my BIOS password is missing. As I went through setting, everything seemed to be on default. And default is not state you wish your alix1d board to be in.
FreeNAS has some issues with ACPI on this board. It will just not boot if you have it turned on. And I had it turned on in my BIOS. Fixing was easy – just turn it OFF. All that wasted time amounted to issue I already knew.
Reason why BIOS settings were changed was simple CR2032 battery. It usually keeps BIOS settings nice and fresh but mine was dead. Any power outage would cause same issues. It was accident waiting to happen.
I checked old invoices and it happens that this system is only two years old. I find it quite peculiar that battery is already gone. There is something that is drinking battery like mad on this motherboard.
Anyhow, everything works perfectly with new battery. I only hope that I will remember this issue when everything fails again in two years. :)