I can confirm the same behavior for Ubuntu 12.10 AMD64 on an ASUS
P8B75-V. My boot drive, sda, is an ssd.

The four mechanical drives run through a single pci/IDE interface.

        sda: OCZ-VERTEX4 (1.5) (ssd, not an issue)
        sdb: Seagate ST380011A
        sdc: Maxtor 6L020L1
        sdd: Maxtor 6E020L0
        sde: Hitachi HDS724040KLAT80

All mechanical drives spindown 60 seconds after signon, as configured in the 
'Disks' gui (ver 3.6.1).
All mechanical drives reliably respond to 'sudo hdparm -S 12 /dev/sdb' (as do 
sdc,sdd,and sde).
All mechanical drives remain asleep until user or program access.

When NOT configured to spindown in 'Disks', all mechanical drives do not
recognize/respond to commands in /etc/hdparm.conf:

        /dev/sdb {spindown_time=12}
        /dev/sdc {spindown_time=12}
        /dev/sdd {spindown_time=12}
        /dev/sde {spindown_time=12}

Also, after a suspend/resume powerdown, all mechanical drives no longer
spindown again unless commanded to in terminal or the 'Disks' gui.

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https://bugs.launchpad.net/bugs/1073137

Title:
  time-controlled spindown with hdparm

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