I'm still not sure what is issuing the hdparm -S 12 command, but adding hdparm -S 0 to the beginning of /usr/lib/pm-utils/sleep.d/95hdparm-apm issues the -S 0 command after the -S 12 command, so it's a workaround.
I'm still not sure what is issuing the hdparm -S 12 command, but adding hdparm -S 0 to the beginning of /usr/lib/ pm-utils/ sleep.d/ 95hdparm- apm issues the -S 0 command after the -S 12 command, so it's a workaround.