Open my computer, rt click on your hard drive, choose properties, go to the tools tab, click the check now button, check both boxes,(auto fix errors and Scan for and attempt recovery of bad sectors), click scan. A dialog box will pop up asking if you want to schedule a scan on your next start-up, hit yes. Now shut down,(don't restart), then start your system again. Note: Some older versions of Zone Alarm will not allow chkdsk access to the drive on start up. If this happens you have to disable the load ZoneAlarm on start up option in the program, just remember to re-enable it later.
The NTFS system has some well documented, but poorly managed issues.
One was corruption of data on shutdown/hybernation in drives larger than 160gb. http://support.microsoft.com/default.aspx?scid=kb;
[LN];331958. There have been some who feel this also affected smaller drives. It also has issues with frequent errors in the security discriptors found with check disk and other diagnostic programs. Check disk is known to have problems checking an active drive. Whenever a file in use is written to by a program, check disk thinks there is corruption because the files values have changed, this will give you the MFT allocation error.
If you have SP2 installed, the 160gb issue patch should already be installed. If you run check disk from the GUI on start-up and it doesn't find errors, don't sweat it, it's a glitch. I know I didn't ask, but you also have to make sure you've scanned for any viruses with the most recent virus definitions.