As I told you, hopefully I'm wrong about this. But that's the only thing I can figure out, with the reason you wrote here. When you can't delete or touch those files, it's almost every time because they are in use. When you enable a virus scan, you are not using many other programs at the same time.
The only thing I can figure out is to google for the antivirus program called: "Avast". Free of charge. Avast starts a scanning before windows starts up, and delete/repair broken files, before windows take those files in use. Maybe that can be a solution, if not, maybe your Virus program can be set-up to take a virus scan, before Windows starts. But hopefully the system files are ok, so that you don't need to take full recovery of your computer.
I'm looking forward to listen to the solution of this problem.