i've been getting a similar error for about a year now on my laptop. The
symptom is that the system will freeze for about 45 seconds, and will
respond to nothing during that time. Afterwards it snaps out of it and
returns to normal operations. When it started it was happening about
once per hour, but with the newer gutsy releases it's been happening
every 5-10 minutes, which makes using interactive programs extremely
annoying. dmesg says:

[17063.276179] ata1.01: qc timeout (cmd 0xa0)
[17063.276201] ata1.01: exception Emask 0x0 SAct 0x0 SErr 0x0 action 0x2 frozen
[17063.276216] ata1.01: cmd a0/00:00:00:00:20/00:00:00:00:00/b0 tag 0 cdb 0x43 
data 12 in
[17063.276221]          res 51/20:03:00:00:00/00:00:00:00:00/b0 Emask 0x5 
(timeout)
[17068.312038] ata1: port is slow to respond, please be patient (Status 0xd1)
[17073.292096] ata1: device not ready (errno=-16), forcing hardreset
[17073.292104] ata1: soft resetting port
[17073.644198] ata1.00: configured for UDMA/100
[17073.832048] ata1.01: configured for UDMA/25
[17073.832064] ata1: EH complete

It's an Acer Aspire 9410 laptop. hdparm says:

ATA device, with non-removable media
        Model Number:       WDC WD800UE-22HCT0
        Serial Number:      WD-WXE406119580
        Firmware Revision:  09.07D09

i'm running the current (as of today) gutsy, and have been updating
regularly for over a year (mainly in the hope that this problem would go
away).

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Santa rosa , strange messages  in the kernel log
https://bugs.launchpad.net/bugs/120839
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