16 Bit Windows Subsystem

I have XP Pro running a Geovision 800 Multi-cam System, which works well. I have been trying to use a registry cleaner and it seems removed something wrong as now when I try to reload the Geovsion I get the above titled message which continues:

"D\WINDOWS\SYSTEM32\CONFIG.NT
The System is not suitable MS-DOS & Microsoft Windows applications. Choose Close to terminate the application"

Does this require re-installing XP? Can it repaired without removing all my files etc. to one of my exterior hard Disks?