Run chkdsk with its most thorough options
As mentioned above, Startup Repair runs a very basic version of
chkdsk, which tries to find filesystem metadata corruption. While that's a good place to start, it's not anywhere as effective as running the utility with its more thorough options. For that, go to the command prompt and enter
chkdsk X: /f /r /b (replacing the
X with the driver letter from your system drive -- note that WinRE might have assigned D: or E:, and not C:, to your system drive). By performing this thorough
chkdsk, you'll fix all errors on your hard disk, such as file system metadata and security descriptors.
chkdsk will also check the entire volume for bad clusters, recover what's there to recover, and mark the clusters as bad in order to avoid new information being written to them.
Run memory diagnostics
Windows Memory Diagnostics, also part of WinRE, finds defective memory modules. Launch it and set it to "Restart now and check for problems." If it finds anything and you've got more than one RAM chip, try to remove one of the modules to see which one's not working.
Use the offline System File Checker
As mentioned above, the System File Checker will scan and repair the most critical system files. However, if Windows itself is too damaged, you might not get to Safe Mode at all. In such a situation, you can use an offline version of System File Checker to inspect your damaged Windows installation from inside WinRE. Type
SFC /scannow /offbootdir=d:\ /offwindir=d:\ (substituting the correct drive for your Windows partition for
d if needed).
Restore the MBR and fix your system partition's start sector
Your master boot record may be damaged in case of a sudden power failure, or if you try to run Windows XP on a newer machine. To restore the MBR, boot into WinRE using your Windows DVD, the recovery CD, or a flash drive (see above) and go into the command prompt. Use the following commands to rebuild your MBR:
bootrec /fixmbr bootrec /fixboot
Now that your MBR has been wiped clean, you'll need to rebuild the Boot Configuration Data, as outlined below, to set the boot information back up.