If ntds.dit gets corrupted or deleted or is missing or whatever it is ! you have to manually backing up !
* Reboot the domain controller and press F8 to display the Windows 2003 Advanced Options menu.
* Select Directory Services Restore Mode and then press ENTER.
* Select the correct installation, and then press ENTER to start the boot process.
* Logon using the administrator account and password you specified during tis process. When you ran Dcpromo.exe to install Active Directory, it requested a password to be used for the Administrator password for Active Directory Restore Mode. This password is not stored in Active Directory. It is stored in an NT4-style SAM file
* Click OK.
* Click Start > Programs > Accessories > System Tools >click Backup.
* Select the Restore tab.
* Click the + symbol next to the following items to expand them:
o Media Created
o System Drive
* Click the NTDS folder to display the files in the folder.
* Click to select the ntds.dit check box.
* Leave the Restore files to box set to Original Location. If you restore to an alternative location, you will have to copy the ntds.dit file into the %SystemRoot%\ntds folder.
* Click Start Restore.
Hope after that all process are okay !