Usually when harddrives make clicking noises, they're near their end.
But as you say it's only in config USB loader and not anywhere else, so maybe the loader isn't constantly asking for the drive to be active.
My own harddrive makes a (pretty loud) click when it's turned off but it's constantly powered when turned on (no matter if the USB is connected or not) so I can't tell.
(By the way, also a Western Digital only 3.5" IDE drive in an enclosure. :P)
I don't know the exact drive, but if you can connect external power I would try that.
Also I'm not sure if that drive got power saving settings or so, you might wanna try disabling that kind of behavior and see how it responds.