Which version of Windows are you running? I have found that with XP if you set your BOOT.INI to /NOGUIBOOT, when CHKDSK is run at boot up it is run blind and then Windows XP starts. You do not get any indication as to the result of chkdsk.
If this is your situation run MSCONFIG from the Run option off the Start button. On the BOOT.INI tab untick the /NOGUIBOOT button. You will need to reboot and this should clear your problem.