If I had to guess what your sound is I would say it sounds like the heads are trying to park or are parking over and over again. While you are scanning the drive the head is not going to attempt to park. Just a thought, try turning off "Put hard disks to sleep when possible" in System Preferences > Energy Saver. If that works then it is a good thing you have already ordered the new 3TB drives.
I have heard an optical drive make a somewhat similar repetitive sound when it was attempting to eject a disc and either the disc or the tray (depending on whether it was a tray or slot loader) was stuck and could not open/eject. If the sound is coming from the optical drive you could probably feel the clunks if you touched the face of the drive or tray.
It is amazing how much disk space media files — audio and/or video — can take up, I recently moved all my iTunes files to an external drive because the 1.1 TB Fusion drive in my Mac mini was filling up. It works well, but the delay loading a tune waiting for the drive to spool up after it has gone to sleep is annoying.
