I have a similar problem and I think it is to do with assumptions that
grub makes.

I have an IDE hard disk which should be hd(1,0)
I have a SATA hard disk which should be hd(0,0)
as the SATA disk has the MBR on it and the BIOS looks at this disk for an MBR 
first.

Every time there is an upgrade to grub or the kernel they get changed
around and I have to manually edit the boot loader at boot else it
cannot find the hard disk drive.  Minor inconvenience for me.

Interestingly the IDE hard disk used to come up as /dev/hda but now it
comes up as /dev/sda (Ubuntu 6.10 and before), the SATA disk coming up
as /dev/sdb.

I don't know why this happens but I guess it has something to do with
the way the kernel identifies drives.  So basically, I'm thinking grub
makes the choices it does because of underlying works in the kernel.

What I do to boot:
  -  Selecting the option you want to boot
  -  hit e to edit
  -  change the hd(1,0)<>hd(0,0), hit b to boot.  
This should work if its doing the same thing that happens to me.

If you need any more info feel free to contact me.

-- 
Installation to second disk confuses drive numbering
https://bugs.launchpad.net/bugs/45989
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