I use Intel's XTU occasionally and while it has it's advantages, i discovered it created some conflicts in my BIOS and some instability - so i only install when i want to run it, then un-install it after use.
I figured it was just my ASUS BIOS, on a Z97M-Plus mobo, wasn't the most stable to begin with - but settings would change unrelated to what i had done in XTU. When i un-stalled, settings quit changing