When operating on battery power (not AC), multiple ATA failures occur.
This issue was not present in 3.0 (stock Ubuntu 11.10 x86_64 build) but is observable in Ubuntu 12.04 beta 2 (3.2.0-23).

The issue also occurs in Ubuntu 12.04 daily (17/04/2012) with latest Ubuntu mainline kernel (3.4 rc3).

The issue occurs both when booting under battery power and when booting under AC and then switching to battery.

Under AC power, no issues are observed.

The system will function correctly for some time (up to a few minutes) then applications will stop responding. The following occurs in dmesg when the issue presents (after which the system begins functioning normally for another few minutes).

[ 238.848502] ata1.00: exception Emask 0x0 SAct 0xf SErr 0x0 action 0x6 frozen
[ 238.848526] ata1.00: failed command: WRITE FPDMA QUEUED
[ 238.848548] ata1.00: cmd 61/00:00:3f:e1:00/04:00:19:00:00/40 tag 0 ncq 524288 out
[ 238.848552] res 40/00:00:00:00:00/00:00:00:00:00/40 Emask 0x4 (timeout)
[ 238.848563] ata1.00: status: { DRDY }
[ 238.848571] ata1.00: failed command: WRITE FPDMA QUEUED
[ 238.848589] ata1.00: cmd 61/00:08:3f:e5:00/04:00:19:00:00/40 tag 1 ncq 524288 out
[ 238.848593] res 40/00:00:00:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 238.848602] ata1.00: status: { DRDY }
[ 238.848610] ata1.00: failed command: WRITE FPDMA QUEUED
[ 238.848628] ata1.00: cmd 61/00:10:3f:e9:00/04:00:19:00:00/40 tag 2 ncq 524288 out
[ 238.848632] res 40/00:00:00:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 238.848640] ata1.00: status: { DRDY }
[ 238.848648] ata1.00: failed command: WRITE FPDMA QUEUED
[ 238.848666] ata1.00: cmd 61/00:18:3f:ed:00/04:00:19:00:00/40 tag 3 ncq 524288 out
[ 238.848670] res 40/00:00:00:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 238.848678] ata1.00: status: { DRDY }
[ 238.848696] ata1: hard resetting link
[ 248.860425] ata1: softreset failed (device not ready)
[ 248.860450] ata1: hard resetting link
[ 258.872300] ata1: softreset failed (device not ready)
[ 258.872322] ata1: hard resetting link
[ 269.448629] ata1: link is slow to respond, please be patient (ready=0)
[ 270.232426] ata1: SATA link up 3.0 Gbps (SStatus 123 SControl 300)
[ 270.244974] ata1.00: configured for UDMA/133
[ 270.260214] ata1.00: device reported invalid CHS sector 0
[ 270.260239] ata1.00: device reported invalid CHS sector 0
[ 270.260256] ata1.00: device reported invalid CHS sector 0
[ 270.260272] ata1.00: device reported invalid CHS sector 0
[ 270.260297] ata1: EH complete

I tried exiting early from /usr/lib/pm-utils/power.d/sata_alpm, thinking this was a SATA ALPM (via pm-utils) issue however this did not help.

I have tried changing the HDD and SATA cable to rule out a coincidental hardware failure however the issue persists. Switching back to Ubuntu 11.10 resolves the issue.

My SATA controller is as follows:
00:11.0 SATA controller: Advanced Micro Devices [AMD] nee ATI SB7x0/SB8x0/SB9x0 SATA Controller [AHCI mode] (rev 40)

The machine in question is a Sony Vaio Y-Series VPCYB2M1E with AMD E-350.

(NOTE: This bug has also been filed on Ubuntu Launchpad  - https://bugs.launchpad.net/ubuntu/+source/linux/+bug/984308)