Microsoft : \WINDOWS\SYSTEM32\CONFIG\SYSTEM is missing or corrupt

Restore the registry manually

1.Insert the Windows XP setup CD and restart the computer
2.Press any key to boot from the CD
3.Press R to access Repair Console
4.Enter the Administrator password. When the Command Prompt appears, type the following commands, one at a time and press Enter after each command, replacing C: with the Windows’ drive letter:

Backup current file to temp folder:

md tmp
copy c:\windows\system32\config\system c:\windows\tmp\system.bak
copy c:\windows\system32\config\software c:\windows\tmp\software.bak
copy c:\windows\system32\config\sam c:\windows\tmp\sam.bak
copy c:\windows\system32\config\security c:\windows\tmp\security.bak
copy c:\windows\system32\config\default c:\windows\tmp\default.bak

Delete corrupt file:

delete c:\windows\system32\config\system
delete c:\windows\system32\config\software
delete c:\windows\system32\config\sam
delete c:\windows\system32\config\security
delete c:\windows\system32\config\default 

Copy file from repair to system32\config:

copy c:\windows\repair\system c:\windows\system32\config\system
copy c:\windows\repair\software c:\windows\system32\config\software
copy c:\windows\repair\sam c:\windows\system32\config\sam
copy c:\windows\repair\security c:\windows\system32\config\security
copy c:\windows\repair\default c:\windows\system32\config\default

5.Exit
6.Enter
7.Restart computer

source : https://neosmart.net/wiki/windows-system32-config-system-missing-corrupt/