That's why I love finding information in the IT world. Given the symptoms, assume it's hardware related, and try the SATA system. New cable (shorter?), new PCI controler card even, update SATA controler drivers, update BIOS, and maybe even a motherboard RMA for faulty onboard SATA.

I've heard so many bad things about onboard IDE RAID drivers of years gone by that I'm nervous of these "new fangled" onboard controlers. The SATA doesn't happen to be a Promise chipset, does it, because that's what has a bad rap in my book for IDE RAID controlers.

Maybe newsgroups and forums discussing your motherboard (typically by manufacturer; alt.comp.periphs.mainboard.*) will reveal common problems similar to yours. Good luck.