It almost seems like a problem with the way that GRUB is reading the
drive.

I say this because you can try to cat /boot/grub/grub.cfg and it's not
reading out the right values. If you boot a USB stick while the drive is
in AHCI mode, you can cat out those values using the kernel AHCI driver
without troubles.

For example:

In AHCI mode, when the problem reproduces, run the following from the
grub prompt:

ls (hd0,msdos1)/boot

....grub can't find anything in the /boot directory at all in the
majority of cases. If, by chance, you do happen to see a grub/grub.cfg
file, running:

cat (hd0,msdos1)/boot/grub/grub.cfg

...will read out garbage on the console.

In ATA mode, where the system boots fine, at the grub menu,  get to a
grub prompt and run the same command. You'll see that grub *does* see a
grub/grub.cfg and you can cat (hd0,msdos1)/boot/grub/grub.cfg
successfully.

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https://bugs.launchpad.net/bugs/741799

Title:
  OS fails to boot certain SATA drives in AHCI mode.

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