Emergency head retracts makes a noise. Generally, this occurs during a dirty shut down when power is suddenly removed from a spinning hard drive. To prevent a head crash, drives park their heads while the platters are still spinning.
Your motherboard is "aware" of a soft shutdown and sends the appropriate command to SATA ports to park hard drive heads gracefully. I'm guessing that your add-on HBA card is not doing the same thing. While there is a distinctive "click", I wouldn't worry about it. Your drives are doing what they're designed to do.
I forgot to post here in case anyone else was wondering, I did find a solution to this via google.
According to another page I found, these emergency head retracts are quite harsh on the HDD and will ultimately reduce its lifespan. I added this little script to startup that seems to allow the discs to gracefully power off again as they used to before I started using the HBA.
If anyone sees a problem with this script, please feel free to let me know and why it's a problem (so I can learn :))