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Yeah, support for the X58 chipset is really sketchy at times, specially with early Linux kernels and drivers!
You will probably find it's down to lack of drivers in the kernel, it's usually the USB that fails for me in some situations.
I do tend to run my SATA settings as IDE in the BIOS though and don't normally have problems with anything. I think I came across some problems some time ago with a Linux distro when I had the BIOS set to AHCI, can't remember fully but it did disable the drives if I remember right.
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