So when you reboot and when you reset both case you loose the settings , right ?
It shouldn't matter on a normal working system to try to change anything. Unless you MB is bad , or using improper case.
I got this MB from ebay that don't report CPU temp to IPMI , so unless is on full speed it will overheat, so I am trying to sett little bit lower the speed, so it's not too loud, it's for testing anyways. My main system is all new and working fine, so no need to touch anything , ipmi regulates speed automatically when set standard.
P.S. In your case you are not trying to cool the cpu , but your hdd , interesting ?! Something wrong with the case ?