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I would be very careful to upgrade to BIOS 0039. The BIOS 003x series have a lot of problems with the i7 2xxxK CPUs. The problem seems to depend on the CPU type and the board. I have a i7 2600K and lost the option to be able to configure the clock ratio reliable with the 003x series BIOS. I already received a replacement board but the issue remained the same
There is NO option to downgrade from 0039 to 0028!
I would check first if there is a firmware update for your SSD. This could also be the cause.
Another option would be to put the drive mode in RAID in the BIOS. Using a drive in non-raid mode is fine. Intel has just recently released an updated Rapid Storage Technology driver (you problem may also be caused by a not correctly shutdown of your SSD). This is a documented problem of the M4 SSD for example and I have seen this also a couple of times. SSD is gone and it takes 1/2 hour before it can be seen in the BIOS again.
KKM, according to the release notes, this issue should be solved by installing BIOS 0039; however, I would recommend you to install all previous BIOS versions in order to avoid any other issue.
Something very important for you to know is than once you install BIOS version 0035, it will no longer be possible to downgrade the BIOS to version 0028 or earlier.
Which is the behavior of your system if you switch the regular hard drive to the SATA port where the SSD is connected? Could you try the black 3.0 SATA ports just for testing purposes?