I had the same problem and configuration, but in my case, after I set the option back to RAID, it still wouldn't boot. Wound up having to reinstall WIndows. Fortunately, I didn't lose any data, just had a major inconvenience.
- Why did the BIOS update indicate a successful update, but not actually install the first time?
- Why does it change the SATA setting to AHCI after a successful install?
At the very least, there should be a warning, but in my opinion, the various BIOS options should never be reset as a result of an update.
My configuration was:
2 1TB disks configured as RAID1
Windows 7 Profesional 64 bit
In my opinion, this is a bug in the BIOS update. With my prior Intel board, I updated the BIOS a number of times without ever having a failure, or having a setting change in the process. This was the first time I updated a DZ68DB, and you're right, after I wrote my original post, I ended up discovering that all the BIOS settings had reverted to their defaults, not just the RAID.
I very much doubt that Intel deliberately released a BIOS that resets everything to the default settings, but didn't document that on the download page or in the readme or release notes. So this was either a dumb luck, corner case scenario that only you and I ran into, or a bug. I'm running a very similar configuration to yours - just SRC instead of RAID 1 - so I'm hard pressed to see how you could blame our hardware or anything specific to our systems.