Windows XP - Config.nt not suitable

Recently some files were downloaded onto my PC without my notice from the internet. I've changed by firewall settings to prevent this from happening again. I've unistalled the applications and all files included from that session but since I've begun to have problems with an application that ran great the day before comes up with the following error "C:\Windows\System32\Config.nt System file not suitable for running MS-DOS and Microsoft Windows Applications." If you choose close or Ingore the error disappears and the application doesn't load. I tried to unistall and reinstall the application but get the same error when trying to install the application. I've tried deleating the config.nt file but still no use. This application although old, is still a very needed application until I can find a replacement and convert all data to the new appliacation. Any idea's or suggestions? - THANKS!