You don't say which operating system you're using; the following is for XP.
You can run chkdsk from your start button.
Click 'Start'.
Click 'Run'.
In the little window type cmd
Click OK
you will now see a small version of what looks like a DOS window. The last line will be something like
C:\Documents and Settings/ a name>
type at the end of this line chkdsk /f
Press enter
It may tell you it can't do the chkdsk now for whatever reason and ask if you want chkdsk to run on the next bootup and give you a choice of Y/N.
Type Y next to it and press enter.
If you then get the C:\Documents and Settings line again type exit at the end of it and press enter.
This will close the CMD box,
Restart your computer and you'll get a lovely blue screen telling you its doing a chkdsk.
Let it finish and it should then proceed to restart windows.
There's no guarantee it will solve your initial problem but at least you will get the chkdsk done, which is what you wanted.
The other thing you can do is do a system file check.
You will need the operating system installation disk in the optical drive. It will want to start installing but as soon as you get the menu, click on the exit or quit button.
You just want the disk sitting in the drive doing nothing.
As before, Press Start.
Click Run.
In the little window type sfc /scannow
Click OK
You'll see a little window in the middle of the screen telling you it's checking your system files. If necessary it will pull off the disk in your CD drive any files that need repairing.
It takes a little while so go and have a coffee or something.
When it's done, the little window will disappear, so you can retrieve the disk and put it away safely.
Good luck with it.