We got following problem with two X9SCM-II-F boards:

After BIOS flash to version 09/17/12 the system is going to loose several configuration settings.
E.G. DVDROM is not in boot order anymore. Hard disks are not displayed in RAID configuration in BIOS etc.
So it is not possible to boot from DVD.
First we thought it's a hardware issue but we got this error on two systems with the exact same hardware.

We flashed from BIOS version 04/16/12 to 06/08/12 and afterwards to 09/17/12.
Using X9SCM-II-F boards.
With Panasonic UJ890 DVD ROM connected to SATA Port 6. (used Port5 too no difference)

After BIOS flashing the system got all configurations and it is possible to see the hard disks and DVDROM in boot order.
After a restart there is only the UEFI entry.
Please keep dvd-drive connect to SATA 5 or 6.

Can you change following BIOS setting?
Advanced --> PCIe/PCI/PnP configuration --> Launch Storage OpROM policy --> Legacy only Advanced
Chipset configuration --> Integrated IO configuration --> Detect Non-compliance device --> enable Advanced
Boot feature --> INT19 Trap response --> Postponed
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