I was browsing the changelog for 2.6.21-rc2:
http://www.kernel.org/pub/linux/kernel/v2.6/testing/ChangeLog-2.6.21-rc2,
and saw a possible fix for this issue.  Commit: 
e2f8fb72144a9f38d44ccf3f939e939392eda659
 says:
"sata_sil: ignore and clear spurious IRQs while executing commands by polling
    
    sata_sil used to trigger HSM error if IRQ occurs during polling
    command.  This didn't matter because polling wasn't used in sata_sil.
    However, as of 2.6.20, all IDENTIFYs are performed by polling and
    device detection sometimes fails due to spurious IRQ.  This patch
    makes sata_sil ignore and clear spurious IRQ while executing commands
    by polling."

I haven't tried this new kernel, but could if that is necessary.

-- 
Sata Drive Not Detected
https://launchpad.net/bugs/81595

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