I'd make sure you don't have the power rail on your PSU overloaded. Unplus your CDROM/DVD and/or move some of the drives to another cable group and see if that resolves it.
That sounds almost exactly like my brother's issues he was having due to too many drives on the same power rail. Strange reboots, intermittent ability to install Win7, drives would usually detect but then mysteriously disappear from the OS, etc.
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