I believe I know what's going on here, and never thought about it happening on a X79 board, but it's obvious to me now that it can. First, some info for you.
Your board has two separate, independent SATA controllers/chipsets. One is part of the X79 chipset, providing two SATA 6Gb/s ports, and four SATA 3Gb/s ports. That controller basically uses the Intel RSTe driver, and now recently a version of the standard Intel IRST driver can work with it too, which you seem to be using. You could use the standard Windows msahci driver on the X79, but that does not provide RAID. Both of the Intel drivers provide RAID.
The second SATA controller is the ASMedia 1061 chipset, which uses the ASMedia AHCI driver, or can use the msahci driver. The ASMedia driver ONLY works on the ASMedia controller, and the RSTe and IRST drivers only work on the Intel controller. They are not redundant, both are required to have both of your SATA controllers functioning. That is the normal way this is done, two separate SATA controllers, each with their own driver. They also have their own connection ports, as you know.
Now we get into the interesting part. Your problem is you cannot get the Intel IRST user interface to run in Windows, correct? It won't start automatically as it should, or if you try to run it manually, via its entry in Control Panel, it either fails with an error message, or simply nothing happens. As you said, other people are experiencing this, and I have too, it is a real issue and seems to be a bug in IRST.
The story does not end there. I was posting in a thread in Intel's forum about this issue, and one guy seemed to find a workaround that got the IRST UI working again. I tried it, and it works. Some other users in that thread said the workaround did not work for them, I don't know why, might be due to their boards for some reason. You'll need to test if this workaround works for you, and in your case you have another option. But, the workaround is not perfect, and is an annoying compromise.
It turns out that if you disable the ASMedia SATA controller in your BIOS, the IRST UI in Windows magically works again. I've tried it disabled and enabled again, and the IRST UI will work when the ASMedia controller is disabled, and does not work when it is enabled. On my board if the ASMedia controller is enabled, but has no drives connected to it, the IRST UI works. As soon as a drive is connected to an ASMedia port, the IRST UI fails. That really makes no difference, but that's what happens on my board.
Not a great fix, is it? Frankly, I don't have a X79 board, so you'll need to try this for yourself, if possible. But this only happens with the IRST driver, version 11.6 or greater. I never had this problem with any of the earlier versions of IRST. The new versions are the only versions of IRST that will work with the X79 chipset, right? If you use the RSTe driver, you should not have this problem.
The good news is the IRST UI that can be run during POST, by pressing Ctrl i, still works with the new versions of IRST. You can use that to configure a RAID volume, and still have the ASMedia controller enabled. Not the same as the IRST UI in Windows, but better than nothing.
Any questions if you actually read all of this?