You may need to run a CHKDSK or an even more intensive drive scan. If you have an Install Disk, you can boot from that and go into the Command Prompt and run CHKDSK /f from there on the system drive.
If you have no Install disk you can try to get into Admin Safe Mode or safe mode command prompt and run it from there.
If this does not help, there are tools on Hiren's Boot CD that can scan your whole drive for read errors, I'll show you how to do that if a regular CHKDSK fails.
You may also want to look at the Startup Items in your Task Manager, and shut down anything you do not need. Just right-click anywhere on your Tray and choose "Task Manager" and go to StartUp - You might want to make a screen shot of what's in there, so I can see what yo have, that way I can advice you on which ones you can shut down safely.