Windows is connected from C to any drive you have essential programs on. In my case I've named my second disk K, and I can't get it unchecked, just like your F. Boot isn't same as System.
"All of a sudden" implies that you have recently installed something in a way that connects your F to your C. Check your latest installs and get rid of everything you may suspect. It's not necessarily anything dangerous, it may be an attachment you can avoid by being careful when you re-install, it may be something like "let us know..." or "auto-update", "start when Windows starts", or something. Thus, check the settings of newly installed programs, click off any auto-updates.
Like in my case, I don't worry about it.
And do scan your computer thoroughly. With Malwarebytes and CCleaner too, but do not have more than your AV running all the time, security programs may collide.
Auto is a function I've got rid off. Have programs inform you when an update is available, but have yourself to decide. Goes for Windows updates too.