Fun and games! When I build my current PC, it originally had an MSI motherboard which had a fault with the SATA system. One of my data disks kept disappearing and after eventually proving it was the board at fault rather than the disk, I was able to send it back and replace it with a Gigabyte board which (so far) has been solid.

Anyway, I feel your pain with trying to diagnose intermittent issues like this. The fault I had took several days of testing, swapping and head scratching until I confirmed what was playing up.

Even though it would cost more if I need a new board, it would be preferable to the hassle of trying to get a replacement drive. But I do need to know what the issue actually is. 

The motherboard is an Intel DQ57TM, LGA1156. It has a Stone Refurb bios, so probably came from an office refresh, but I bought it from somewhere else so it's almost certainly 3rd hand and probably dates back to when the boards were first made 12 years ago. That said, it's been rock solid since I got it.

It probably doesn't help that I have a lot of drives. Maybe I'll work out how to diagnose the problem. Maybe not.

I have just had a thought, I wonder if the last massive Windows 10 update package had something to do with it. I had a boot drive disappear once after an update.

Well, the motherboard's SATA system has problems, in particular the internal e-SATA port that the drive was plugged into, although there have been a few other weird issues that I think are related. The drive itself has come though a complete surface scan and a full SMART scan with no problems. On the other hand, the bios reports that the SATA port is "not installed" which seems fairly conclusive. That said, the "not-installedness" is a bit hit and miss, as I can see errors and warnings in the event log relating to the drive plugged into it.

So, I'm going to limp along using the port previously given to the blu-ray drive until I can source a replacement board. Hey Ho.

Edit: except that didn't work. It seems that this motherboard won't mother this HDD on any port and via any cable. So now I have it attached in an external caddy and it works fine and sits just where it did before in the drive set-up. Maybe it is buggered after all - at least with a SATA connection. Although all the caddy does is provide a standard SATA socket and pass the data through the USB bus.

The drive, that has been cruelly rejected by my Plex box, works perfectly as a SATA attached drive in my main desktop PC. It also works perfectly as a USB attached drive in the Plex box. It's brother, an identical (or so I thought) Toshiba x300 8TB, works perfectly in any socket on the Plex box, and any cable.

I've heard of motherboard drive controllers and channels going wrong, but I've never heard of them developing a grudge against a particular device.

If I can't find anything to fix it, I shall attach it as an internal USB 3 device with one of these, or similar. I can snip the power cable and attach it to the 12V & GND pins from a Molex. That
way it will reboot with the rest of the drives.

Probably get it finished just in time for the motherboard to fail altogether. 
 

I've had several drives that ceased working after a while (usually >2-years), when directly attached via sata or pata motherboard plugs, but work fine in usb enclosures.

I had my first BSOD in aaaaages yesterday, by plugging in an SD card that had been corrupted by a bad Raspberry Pi. One corrupted card completely brought down the OS as the disk management service got stuck trying to interpret it and ignored all other requests. 

Had to disable automount in diskpart in order to access the card and delete the partitions, after which the card worked fine again. 

So yeah, bloody PCs are a pain in the hoop.

Yeah, looking around t'interweb, it seems to be a "thing". Thing is, this drive has now passed a ten hour checkdsk scan and an almost as long SMART scan (HDDScan), and it works perfectly in two different SATA slots on a different, newer, PC. As far as I know, it's only in the old PC with it's 11 year old mobo that it can't be seen. But that said, 4 other drives and a DVD drive work fine, in any slot. So there's obviously something about this particular HDD that stops it shaking hands. And it's something that happened over the weekend.

I've stuck on the latest BIOS and chipset drivers, but without any improvement. It's working OK through USB, and there's a card in a PCIE slot giving USB3 with a spare socket, so I'll mount it inside but connect it via USB.

Yeah, that is SOOO annoying and a real issue with Windows: the way one misbehaving process can hang or crash the entire OS, and there's no way to kill it.