Chkdsk is not the correct tool to use to diagnose hard drive issues (which is what it sounds like you have).
Test the hard drive with a diagnostic utility downloaded from the drive mftr.'s website or use Seagate's SeaTools For DOS. You will create a bootable CD with the file you download. You will need third-party burning software to do this such as Roxio, Nero, or the free ImgBurn. Burn as an image, not as data.
http://www.seagate.com/www/en-us/support/downloads/seatools/seatooldreg
http://seagate.custkb.com/seagate/crm/selfservice/search.jsp?DocId=201271 (how-to)
Boot with the CD you made and do a thorough test of the drive. If it fails any physical tests, replace it.
If the hard drive tests good, the problem is still hardware but a different component. With the computer unplugged, make sure the cable going from the drive to the motherboard is snug. If the problem persists, swap out the cable for a known-good one. Test. If the problem persists, test the power supply. If the psu is good, the problem is on the motherboard. depending on what kind of computer you have, you may be able to use a different drive connector on the motherboard. If that works, then realize this is a temporary solution and make plans to replace the motherboard.
If the computer is still under warranty, you should contact the computer mftr.'s tech support for repair/replacement. I would still do the diagnostics on the hard drive first because if the drive fails the tests you can tell the support tech you've already tested it.
Note: If this question is about the old computer running Windows 2000 which you were replacing, the writing is now On The Wall. Back up your data and replace the machine.
MS-MVP - Elephant Boy Computers - Don't Panic!