Can you skip the chkdsk schedule? You may want to check the SMART status of your hard drive. HDD Sentinel is good for this, although if you can't boot into Windows, you will need to get the DOS version of Sentinel (which is still free), burn it to a disc or copy to a flash drive, and then boot off that. It will relay the SMART data and overall health of your drive.
Hiren's Boot CD also has this program.