As it turns out, I am about 95% sure the SATA controller on the motherboard is at fault. It’s hard to say, because an old SATA I drive that i hooked up to the controller did not fail, but other SATA III drives did report problems upon scanning (of which those problems did not show up after moving to a different controller).
The hard drive which was originally having issues is on another controller now, but appears to have some sector damage now. It has not disappeared in days, but reading new files added to the drive causes teh HD LED to stay lit and whatever read operation was initiated just hangs.
I figured I would update this in case someon else had the problem and wanted to see my symptoms and what eventually happened.
