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Please post your exact motherboard model. You have 2 controllers - one native to the motherboard chipset and one ITE controller (which is probably a RAID controller). They each have their own bios and do not talk to each other.
In your first set of pics, it appears that you have all 3 drives on the ITE. In the second set, you have the hard drive on the native controller and the opticals on the ITE.
With only 3 drives, I'd put them all on the native controller and disable the ITE controller.
The cable error you are getting is because your optical drives are on a standard 40 wire IDE cable, and your DVD burner is actually an ATA-66 device. Either ignore the error or use an 80 wire Ultra ATA cable.
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