Secondary Hard Drives Randomly Disappear

I've had this issue for months now. I chatted with tec support for my motherboard and the guy wanted me to RMA it. I have searched the internet high and low for an answer. Here is the issue:

I have two internal hard drives I use for media. A few months ago both would randomly go away and the only way I could get them back was to reboot. I tried changing cables, swapping sata ports, etc. Nothing worked. I updated bios, made sure all hard drives had current firmware, etc. None of that solved it either.

I ran Sea Tools on my old drives and one came back with an error. So, I purchased the two drives listed in my profile. Set them to GPT and formatted. Swapped all my data over and all seemed to be okay. That lasted a week. Now one of the two drives is randomly going away.

This morning, it seems my SSD boot drive didn't appear during the post as I had the message to insert bootable media blah blah blah. I hit the reboot button and up popped Windows.

Edit: I also changed power settings to never allow the hard drives to shut off. That didn't work either.

I tried all of the software related fixes to no avail. I tried the bios/firmware fixes no go. I replaced old drives with new. Still happening. I really don't want to RMA the board if I don't have to. If anyone has found a fix for this issue I will be eternally grateful.

System:
Windows 7 Ultimate x64
AMD FX 8350
Asus Crosshair V Formula Z
XFX R9 280X BE GPU
16GB Corsair Vengeance 1600 MHz DDR3 9-9-9-24 RAM
250GB Samsung EVO 840 SSD (boot)
3TB Seagate Barracuda ST3000DM001 HDD (media. 2 drives)
Corsair HX 1050W PSU

Hello Archi!

This really doesn't seem like a hard drive issue; you have swapped drives, settings, cables and ports, ran diagnostics and updated BIOS and firmware. Additionally, it can hardly be a HDD problem as you have had a lot of different drives (and a SSD!) that have experienced these common symptoms for a very short period of time.

The only way at this point you can find out if in fact it is the drives (which almost certainly are not), you could try them on a different system, or try a couple other known working drives on your system, and see what happens.

My advice is to RMA the board, and you shouldn't experience this issue any more afterwards.

CK_WD