I recently had trouble running FreeFileSync from computer auto start-up, I kept getting a warning that the app could not write to protected folders. I found that only FreeFileSync.exe was allowed through controlled file access of any protected folders.
Adding RealTimeSync.exe (The first called at computer start-up) cured the problem. Both these .exe are in the same app download folder. Something to look for when downloading multi .exe apps and it doesn't function as expected.
All Settings>Update & security>Windows security>Virus & threat protection>Manage Settings>Manage Controlled folder access>Verify as administrator>Add an allowed app. Or type "controlled folder access" in All Settings search.