Tracking it through more files than I can recall, I found that /usr/lib
/pm-utils/power.d/95hdparm-apm calls /lib/hdparm/hdparm-functions which
includes the following lines:

if hdparm_is_on_battery; then
                hdparm_set_option -B127

Changing -B127 to -B254 seems to prevent APM causing ATA resets on battery 
mode. This method allows the other hdparm values to be set properly.
I'm not sure of the wider implications of this or what has changed since Ubuntu 
11.x (did it also set -B 127? did something else change which has meant -B 127 
causes ATA resets on my hardware?).

If anyone can help get my findings to the correct person/group/project
to resolve this permenantly I'd be most grateful.

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https://bugs.launchpad.net/bugs/984308

Title:
  ATA failures when operating on battery power in Ubuntu 12.04

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