Maybe it wasn't the harddrive?

I've been having problems with a hard drive.  Every boot it would need to run chkdsk.  I have 3 hard drives in, but it was mostly the C: drive needing checking.

I cloned the disk to a brand new HD, but the chkdsks are still happenning.  Files are being corrupted and chkdsk is finding them.  But could it be something besides the HDs going bad?  perhaps the SATA controller or the mobo itself?  The SATA cables perhaps?  How do I find out?

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Is the PC shutting down normally?

Take the drive to another PC and test it with the manufacturer's diagnostic tools - you can find them on the UltimateBootCD.  Swap the cable for another one.  Swap the power supply.  At this point, if it's ok on the other machine but not on this one, I would consider the motherboard.

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This is what you need to do to help your troubleshoot..
Virus scan and perhaps an adware scan as well.
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What wattage is the power supply? If you are running 3 hard disks.
this getting old now but still give you some idea

AMD Athlon 900MHz-1400MHz 50W-72W
AMD Athlon XP 1500-2100+ 60W-72W
AMD Athlon XP Thoroughbred 1700-2100+ - 50W-62W
AMD Athlon XP Thoroughbred 2200-3000+ - 62W-70W
AMD Athlon 64 2800-4000 - 70w-80w
ATX Motherboard - 45W-65W
AGP video card - 40-80W
256MB RAM Module - 20W
512MB RAM Module - 35W
CD-Recorder - 20W-35W
CD-ROM Drive - 20W-30W
DVD-ROM Drive - 20W-25W
DVD-Recorder - 30W-40W
IDE Hard Drive - 15W-20W
Sata Hard Drive - 24W-30W
SCSI Hard Drive - 15W-25W
15,000RPM SCSI Hard Drive - 35W
Floppy Drive - 8W
Network Card - 5W
Modem - 5W
Sound Card - 5W-10W
SCSI Controller Card - 20W
Firewire Controller Card - 30W-40W
USB 2.0 Controller Card - 5W-20W
Case Fan - 3W-5W
CPU Fan - 3W-6W

These are estimates and you should make sure you have more than just enough wattage.
I've seen corrupt Windows 2000 and XP installations cause problems similar to yours.

Try a clean install of Windows on one of your drives and see if problem is corrected.
Test your harddisks when you attach them to a cheap 3rd party pci plugin controller.
If they work, it's the mobo
first you should test what is causing the chkdsk to happen; it can be caused by a dying disk, but also by some other hard or even soft problem.
Memory test :   use memtest86+ from      or from the ultimate boot cd.
Disk test : any of these : (you find some on the cd too)

you can also diagnose by disconnecting hardware.
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