I believe the problem here is that all your BIOS' are configured to use
AHCI. The current Ubuntu kernel is loading it as a module thus loading
it very late. To add to this the kernel has another ATA driver compiled
inside it which interacts with your disk controller and making it act in
this bizare wait state.

After the AHCI module is loaded it fixes everything.

Proposed workaround: Disable AHCI in your kernel, enabling IDE or RAID
as the alternative, this should stop the delay you seem to have. I
tested it on my machine. Test it in yours so I can follow up.

Proposed fix: Compile AHCI into the kernel and not as a module.

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https://bugs.launchpad.net/bugs/297058

Title:
  Consistent repeating [ata1: link is slow to respond, please be patient
  ]

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