I've run into this issue some days ago.
After changing MB and reinstalling system (Windows 7 Ultimate x32) I've noticed the HDD clicks while shutting down my PC.
Then I changed several different HDDs (WD 320, WD 750, Seagate 1Tb) and it was all the same - clicking while shutdown. All HDDs were brand new.
Assuming that drives were ok, I decided to play with BIOS. And after Disabling AHCI (setting Mode to Native IDE) clicking stopped.
In my case:
if Mode = AHCI then HDD clicks
if Mode = IDE then HDD is silent
So just try to disable ACHI and see what happens.
Regarding many threads on different forums on this issue, I suppose that the problem is somewhere in system/
drivers/software but it's not about drives and MBs.