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DH77EB motherboard: HDD shows in bios but not in windows (8.1)

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I have 3 hard drives & 1 dvd R/W on my SATA connections. The DH77 has 6 SATA connections, 1 external & 5 internal. (internal locations 0-4)..The boot drive is on loc 0. I cloned the boot drive yesterday using Acronis & replaced the it with the clone so that the pc is exactly the same but the boot drive is different. Most programs run seamlessly after this but some recognize the drive as different & squawk a little. Roboform is1. The problem now is that SATA locations 2 & 4 will show in the bios as connected devices but do not appear in windows (8.1) after startup. Device manager cannot see them & neither can Explorer. They don't exist in windows.I have not tried the external SATA connection. This is extremely confounding to me. Please help

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Thanks for joining the motherboard community.

I understand you have cloned your boot drive using Third Party software on another drive. Now, hard drives are not visible on Windows.

It appears to be an issue with the software you have been using to create your clone disk. Please bear in mind, your computer supports RAID levels. If you are going to create a clone for one of your drives, you can take advantage of RAID 1. This technology creates a mirror of your existing disk.

See here for more details: