The “save changes/load defaults” popup is often triggered by a failing CMOS battery. Another indicator is the system clock being off.
Depending on the age of the computer and the sophistication of its BIOS your computer can provide you with diagnostics that can tell you of an impending battery failure.
The only “software” changes that could trigger this warning (that I can think of) would be a BIOS firmware upgrade. Did you try restarting your computer again and (if so) did the pop-up reappear?
The machine is a 2 year old Asus X541NA. I will try the restart right now.