Why must this be an issue with Byobu, Gnome or Ubuntu? When I do a little investigation I see a lot of people having similar problems that are using Windows. The problem seems to be caused by the motherboard or the CPU itself.
What kind of benefit do you have when overclocking? Sure stressing operations like video encoding finish a few seconds or minutes earlier at the cost of being unstable and producing corrupt results. Also the hardware wears out faster and that configuration isn't supported by the manufacturer. Everyone wants that of course. And why do you need to monitor your CPU temperature? Sure I did kind of like this stuff 5 years back on Windows with Samurize. But why? If your CPU gets to hot it will either clock down preemptively (bye bye overclocking benefits, we know that since the Prescott days) or the BIOS/EFI will warn you at a specified threshold and will shutdown when passing the second specified threshold. If you're running that box remotely in a datacenter as a server, I hope people like you get extra charged for the amout of additional cooling needed. Just because of urban legends like "yeah compiled my realtime kernel with this special patchset, now our $InsertRandomMultiplayerShooterHere server runs 3 % faster". Absolutely. And if something goes wrong always blame other people, always.
Standard of the shelf hardware with standard configuration doesn't seem to have enough issues these days.