You need to run chkdsk then run Startup Repair up to 3 times.
How to run chkdsk from the Recovery Console
- Boot your Vista or Windows 7 installation DVD
- When you see "Press any key to boot from CD or DVD", press Enter
- At the "Install Windows" screen, click on Repair your computer at lower left
- At the System Recovery Options screen, make note of the drive letter assigned to your boot drive (normally C: ) and click Next
- At the Chose a Recovery Tool window, click on Command Prompt. You will be sitting at X:\Sources directory
- Run chkdsk
- If you did not note the drive letter of your boot disk, you can enter bcdedit and look at the osdevice line to see what it is.
- Type chkdsk c: /r and press Enter (use the letter from above).
Let it run to completion undisturbed.
If you don't have a install DVD, you can download a legal copy here: Official Windows 7 SP1 ISO from Digital River
Make sure you get the same version you have installed: 32 or 64 bit; Home Premium, Pro or Ultimate.
See here: Startup Repair