Have you tried swapping the cables, or checking that they're properly seated? I've only ever experienced one instance of an onboard controller issue. You can always circumvent it if it is faulty by fitting a PCI SATA or PATA interface card (I'd choose SATA, you'll get a bit of extra performance, and the drives are cheap - though you might want to just use your existing PATA drives).
Working fine in an external enclosure doesn't really tell you anything. There's no need to access the boot sector whilst it's in there being accessed by an external copy of Windows.
What you need is to download the Ultimate Boot CD
and test the drives with the manufacturer's specific tools where possible. You'll want the hard drives to be installed in the PC directly, not through the enclosure.
I hope this helps.