Copied from #539467 bug.
I have the same problem:
Multiple ata1.00 errors even when pc is idle on Gigabyte GA-E7AUM-DS2H 
motherboard.
One disk already is dead (Seagate) - it was on Jaunty.
The next was going down (WD) on 10.04 fresh minimal install with nvidia 
proprietary drivers.
Switching off AHCI from bios worked for me as well.
More reports about this issue:
https://bugs.launchpad.net/ubuntu/+source/linux/+bug/217920
http://www.nvnews.net/vbulletin/showthread.php?t=126152

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Multiple ATA Exception Emask, NCQ disabled etc during boot
https://bugs.launchpad.net/bugs/353812
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