Sound bit serious try creating a backup  OF ALL THE SEPERATE FOLDERS

Then run scandisk on all your disks tick both boxes to do a surface scan

Then reinstall run the CFS3 then go back to restore a folder at a time (this bits tells you witch bit messed up)

I'd only do the last bit to i you need to know or have other bits added such as

CFS3 Nationality Expansion Kit ~ Redux Edition
Battle of Britain
addon scenery
No CD
etc

MY Guess is you done a defagment and not ran a scandisk but it some times just messes up

nrev