It does sound like it could be a failing hard disk, or something else wrong on the hard disk controller side of things. I know that a faulty DVD drive on PATA can cause havoc with a hard disk on the same cable, don't know if the same is true with SATA configurations. I've seen the former happen a few times, but not
yet seen the latter.
For testing disks, I find MHDD to be excellent.
http://hddguru.com/software/2005.10.02-MHDD/ It's quite old now, so there's a chance it won't support modern controllers. That said, I've only had one occasion when I couldn't get it to see disks on a PC, and I've used it many times. If you download the ISO image, you can burn a bootable CD (even a floppy!
It's really small!).
Using it you can scan the hard disk surface, and it times how long it takes to read each cluster, and makes you a table of timings. You can spot failing clusters because they take longer to read. It can move data from those clusters, or erase them (though you'll lose data that way!)
If I'm recycling an old disk, I run the scan, note the performance stats that it produces, then use MHDD to erase the entire disk, and re-run the scan. This usually results in improved performance in disk speed!
You can then use it to make a basic partition on the disk, at which point you're ready to install the O/S of your choice.
There's lots of other options too, for measuring average seek time, adjusting the noise vs performance setting that many disks have... it's great. It's only a shame that there's been no further development of it, though it's still powerful in it's current form.
For those interested in the program, I've attached a screenshot I took a while back of a disk I was testing that I'd just bought off ebay.
Looking at the right hand side, you'll see that there were no clusters that took <3ms to read (it's not the quickest of disks!), there were 228246 clsuters that took between 3 and 9 ms to read, and 1578 that took between 10 and 49 ms to read. So it's not too bad, considering it's age. A failing disk would show some speedy clusters, and a few taking 150 or 500ms to read as well. Of course, some might be damaged, and they'll show as bad.
After erasing this disk with MHDD, I had an increase in clusters taking <10ms to read, and a decrease in those taking <50ms, although not by a great amount. But was worthwhile to test the disk was working OK.
Ian