A possible workaround could be an fstab entry with the UUID of the
Freeagent partition. You can get the UUID with 'sudo vol_id /dev/sdX1' .

/etc/fstab entry:
UUID=LONG_NUMBER  /media/MOUNTPOINT  FILESYSTEM  user,defaults  0 0

The user-Option is needed to be able to mount the Freeagent hard disk without 
root permissions.
If you don't want to use the Terminal every time you can write a little Script 
which un/mounts the hard disk and add this to your Panel or desktop.

#!/bin/bash
if  `mount | grep -q /media/MOUNTPOINT`
then
        umount /media/MOUNTPOINT
else
        mount /media/MOUNTPOINT
fi

-- 
external Seagate FreeAgent disk doesn't auto mount
https://bugs.launchpad.net/bugs/126825
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