Base

Process Explorer has a special column that tracks the change of the number of bytes read or written by a process:

You might be able to capture the name of the process that is reading or writing data to your secondary HDD this way.

//Edit:

If you know that it is the System process that writes something to the external hard drive, you could trace what the process is doing in the Process Monitor:

Start/stop the capture with Ctrl+E.

Define some of those filters:

//Edit2:

Maybe you could track the thread ID associated with a certain IRP event and then track the thread that caused that IRP event:

Some background:

SATA drives usually have the following options:

• Hot swap the drive (pull it from a live system, usually to replace it with a new drive after the old drive has failed).
• The ability to spin a drive down and put it permanently in a standby-mode. (Best done before hot-swapping a drive). This mode needs a reset or a power cycle to recover from. (Which is not a problem if you are going to plug in a new drive).
• The ability to set performance modes varying between 'as silent/as energy friendly as possible up to 'max performance and ignore everything else'
• The ability for the OS to ask the drive to go to a low power mode (usually spinning it down). It can recover from this. There is usually a 30-ish second penalty while the drive spins back up.
• The ability for the drive to initiate the same.

Windows solutions:

• Managed via the OS as per Alex Atkinson's post.
• Direct control via some program which asks the OS to send SATA commands. (examples: the commands listed in the question).

Drive solutions:

Change a setting on the drive and let the drive initiate power settings.

There are already several posts on that here on [su], mostly using hdparm. One way to do this would be to boot Linux (or BSD, or OSX) and run hdparm as root.

Or, as found by the OP, there is a windows port of hdparm. Note that you are directly communicating with hardware. This means that you will need to run it with elevated rights.

These settings should stay in the drive, even after you power off the system (annd thus the drive in it). Should you have an OS which does not [only] do its own power management but also tries to reconfigure the drives site (or a non-spec drive configured e.g. for something 'extremely green' then see this post.

Non-windows solutions:

• What do different values of hard drive's Advanced Power Management feature (hdparm -B) affect, except spin-down?
• How do I get my disks to spin down after one hour?