Have a similar problem. I have windows on two sata drives (in a nvraid)
and intrepid on a third drive (non raid). When I boot it drop to the
busybox and initramfs, but if I exit then it boots. But when I log in,
my raid is not present and my /dev/mapper/ only shows control.

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Fails to find boot device in Intel D945Gnt (with Jmicron ATA controller)
https://bugs.launchpad.net/bugs/290153
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