PowerFlower,
The MAC address for the primary LAN port is indeed stored in the BIOS flash (for secondary LAN/WLAN interfaces, though, EEPROMs are typically used). We program the MAC Address into the flash as part of the factory board validation processes. This portion of the flash is then locked down and (in theory) cannot be changed (lost) during normal BIOS update processes. In a word, it should not be possible for the MAC Address to be lost -- well, other than via flash component failure. My suggestion is thus that you contact Intel Customer Support - which it typically done via phone (not email) - and have them replace the board...
This board was part of the last generation that we shipped with a text-based BIOS Setup interface. I assure you, however, that it is still a modern UEFI-compliant BIOS and has all of the same options that the later graphical interfaces expose (though limited by the lesser set of capabilities offered by the Intel(R) Atom(tm) 2500 SOC architecture)...
...Scott