At most features of built-on keyboards like Fn only BIOS is in the control. Most often the OS does not even know about presence of this special modifier key. Some computer models make special features available to their drivers running under the OS, but this is not always true.
Example:
- some features are reachable: in utility supplied by manufacturer of your laptop, you can control keyboard backlight behavior (always on / always off / automatic)
- on the other hand, I haven't seen the case where keypress of Fn was visible to keyboard routines in OS. It is completely hidden from the OS.
In your case I strongly believe this is only the BIOS problem. You can also test it by some neat procedures, e.g. keep your system untouched for few hours (you can also disable scheduled tasks etc.) to ensure no application was launched which could affect the behavior.