Windows wakes up the external hard-drive whenever a software opens directory tree

Been seeing this with a number of drives - 1TB satas - when resuming for s3 sleep.

Check to see if your drive supports s3 sleep mode: Please first check if your secondary drive support S3 in Windows 7:

Step 1:

1. Click the Start button, then in the "Start Search" box, type CMD but DO NOT press Enter yet.
2. In the list above, under "Programs" right-click on CMD that appears above and choose "Run as Administrator" and click "Continue".
3. In the open window, type the following command and press Enter:

Powercfg /devicequery s3_supported

Step 2: Disable write caching on the secondary drive

1. Click the Start button, then in the "Start Search" box, type DEVMGMT.MSC but DO NOT press Enter yet.
2. Right click "Disk drivers/your secondary drive" and choose properties.
3. In Policies tab, uncheck the option "Enable write caching on the device".

Some have fixed this by installing the Intel Matrix storage drivers

Others by forcing the drive from AHCI to IDE mode (bios setting)

My first thought would be to say it's the drive, as they are notoriously crappy drives.

Check this out from NewEgg's feedback section on the drive:

Cons: Vista OS. It worked fine when initially plugged in, but it would not recover after the computer was put to sleep. Upon wake up, the drive would not appear in Explorer. It would reappear again after a reboot but would disappear after a sleep cycle. I wanted the drive to store Media files from Vista Media Center which goes to sleep when not in use. Returned it and bought a Western Digital.

But, you mention you upgraded the chipset drivers, but

1. Did you get them from Asus or Intel? Hit Intel's site and grab the latest version offered by them (currently v9.3.0.1019).

2. Did you update the drivers for the HDD controller itself?

That board also has two different SATA HDD controllers on it, an Intel Matrix Storage controller, and a JMicron.

So hook it to the Intel SATA ports and hit Intel's site to grab the latest Matrix Storage Manager/drivers (which have been renamed to the "Intel Rapid Storage Technology Driver").

Here's a direct link to v11.1.0.1006 of the Intel Rapid Storage Technology Driver from March of this year.