You most certainly have a different issue. Your kernel is not attempting
to load ata_piix or pata_acpi modules. Only the SATA link to your SSD
gives this error. The original bug this happened for every port in the
machine even if a drive is not connected to it. Since you have a brand
new cougar point chipset I am guessing the older AHCI driver is the 35
kernel series is to old. You may just need to use a more recent kernel.

You could try forcing the link speed to 3gbs as both of your drives are
SATA II but it looks like they are connected to the 6gbs STATA3 ports on
the chipset.

If you edit your grub boot line you can add libata.force=3.0 
Not sure if that still works. It used to work on older kernels but I vaguely 
recall reading that ahci module now uses libahci and no longer relies on 
libata. 

or you could try adding libahci.skip_host_reset=1 but I am not sure if setting 
that parameter has any negative consequences.
Anyway you should file a new bug report about your issue as it is different 
that the one in this bug report. On the plus side I see no reason why you need 
to rebuild your kernel so you can revert back to the ubuntu supplied packages. 
Your kernel appears to be correctly discovering all of your devices and loading 
the proper modules.

Cheers

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https://bugs.launchpad.net/bugs/595448

Title:
  Slow boot caused by SATA controller reset

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