When you run chkdsk with either /f or /r on the Windows partition, Windows has to reboot to do the check. To do this, click the Start button, click on My Computer, right-click on the Windows drive, select Properties, click the Tools tab, click the Check Now button. Then, just check Fix errors, click the Start button, click okay to the check on next boot and then reboot. Then, when you're back in Windows, open the Command Prompt and re-run a regular chkdsk and post those results. If it shows the errors have not been fixed, then chkdsk is unable to fix them.