The click is just like the click that happens when you start up the karma, right after the spinning Rio logo.

Wait a minute... All this time I'm assuming the click is coming through the headphones.

Is this a physical clicking noise made by the hard drive instead? To check this, unplug the headphones while playing a song, and see if you can hear the player itself making the click.

If so, an occasional single click is normal as the hard disk spins up and spins down. Repeated clicks would indicate a failing hard disk.