The file structure may be corrupt and Windows is incorrectly showing disk usage.
Go to Start > Run and type 'command', this will bring up the command prompt. Whe you have that type 'chkdsk' and see what it says. If there are a few file errors you can repeat again, typing 'chkdsk /f', if there are loads of errors type 'chkdsk /r'. Both these will ask if you want it to run the next time you boot - say yes to that.
If there are no errors from chkdsk, we'll have to think of something else