This is a known issue and a software problem.. Not an O/S or hardware problem.
Main reason why this occurs is that saved O/C profiles are loaded after a custom BIOS is flashed and since the custom BIOS values are different, the saved profile setting are invalid. You end up with crazy settings that appear stuck.
Don't worry, it is a matter of finding the right software/settings to remove.
(1) Uninstall ALL O/C apps and you MUST choose to remove ALL settings/preferences/profiles. You may need to manually hunt down where the settings are stored and MAKE SURE they are gone. Reboot and then re-install the O/C app "fresh"
(2) FULLY removing all drivers and re-installing using a "CLEAN" install has reported to resolve the issue.
(3) Geforce experience was reported (I haven't ever confirmed this personally) to cause this issue after removing and re-installing it reported to resolve.
TIP: ANYTHING that may communicate with your GPU in ANY WAY is a suspicious app that should all be uninstalled. This is a GLITCH and NOT a software bug. Once you resolve the issue removing the offending software SETTINGS, you can just re-install the APP and it should work just fine.
I have had this EXACT issue with MSI Afterburner and after I resolved it, I put MSI AB right back on with no issues. It was just a saved parameter that needed to be removed.
Happy hunting! Report back please.