Something is wrong then. It could be a damaged file table that is causing the updater to error out.
Boot to your OS X installation disk. Don't install OS X, but when the interface gives you the opportunity, go to the menu bar and run Disk Utility. Choose your hard drive in the left column and then press the button at the lower right to "Repair Disk". If it shows any errors, repeat the repair procedure until it comes up clean.
If there are any disk errors reported, and Disk Utility cannot repair it after three or four tries, you're going to have to use something more suited to the task.
Disk Warrior is probably the best program available for that.
If Disk Utility reports no errors, then I would continue on with an Archive and Install of the OS. Make sure to use the option to preserve your settings. After the installation is complete, apply all available updates.