I believe this is probably related to Bug #46520 in which IDE disks and
SATA disks are handled in differing orders between OS and BIOS/grub.
This bug is easy enough to work around in exactly the way you did in all
cases, but it really would be good to get it fixed, as this seems to
affect everyone who has both SATA and IDE disks, regardless of
configuration.  Hopefully we can get this whole situation well enough
documented that the devs can get it properly fixed.

Tor

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Hardy Install constructs GRUB config incorrectly when using PCI RAID card with 
IDE drives attached to it
https://bugs.launchpad.net/bugs/255647
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