Long story short, after instant flash, Thunderbolt card wasn't showing up on System Browser.

I realized advanced chipset option, Intel Thunrderbolt was disabled. So I enabled that, and another selection occurs right beneath it by default says "Unique ID"

Then I started having issues with booting, restarting, I went ahead and tried changing CSM settings as limited info online says Thunderbolt card may have issues with that CSM 

As I was trying different things, I realized let me just instant flash back to BIOS version 1.10 which I remember Thunderbolt was recognized, even though it was an older BIOS version

It successfully instant flashed, but now reboots to black screen, I can't even see the AsRock Logo to press F2 to see whats going on after instant flashing the Bios back to 1.10

I am really confused. What's going on ? 

PS. I disconnected the Thunderbold 2 AIC AsRock Card and tried again as well, just to see, Nothing changed.

Please Help!

Thanks

See my post under the image of your board if that does not work.

Looking at the image I posted the BIOS selection jumper is next to the CMOS clear jumper.

Should I restart? should i do the whole reset again??

And relax, being stressed will only lead to mistakes  There is nothing to worry about so far.

I pressed cmos button and then started the power, now it is doing that thing again, on and off for 2 seconds intervals, it is been doing it for 2 minutes, Should I let it just go on? How long it would take, 

After how long should I ever worry? it is been almost 3 minutes now...

It should power on, remain on for a few seconds then power off and back on then post.

Do I wait? Do I do anything with CMOS Battery, or do I just plug things back on to power?

ftp://europe.asrock.com/Manual/X99%20Extreme4.pdf" rel="nofollow -

ftp://europe.asrock.com/Manual/X99%20Extreme4.pdf" rel="nofollow - Here is the user manual for your board, look at page 20 for steps to reflash BIOS_A to the backup version. Once you have done that you can go ahead and set the BIOS_SEL1 jumper back to it's original position and try to post again. If all is well then go ahead and flash to the BIOS version that worked best for you.

Hopefully the mac address issue will resolve itself once you are back on BIOS_A, if not we will have to look at fixing that too. The recorded Mac address in BIOS_B must differ from the one on BIOS_A....

The option is under the "tools" tab.

Once it completes power off and switch the jumper back to pins 1 and 2.

If all went as it should you should now be back to posting normally. If the Mac address error pops up again when on pins 1 and 2 let me know and I will have to look up how to fix that.

However it went back into the same messages, now it is still on the alternate pins, I am on UEFI BIOS again should i just hold power button and turn everything off and unplug everything to switch the pins and go from there?

Pity about the Mac address issue, that just adds more work to be done.

https://www.youtube.com/watch?v=wGVhkgtTc0w

It isn't a major issue however and does not indicate a problem with your board 

If you want we can try and perform the process together but I must warn you I am not overly familiar with the tool.

There is also another sticker that should be on the top of the rear panel audio jacks, that is also a 12 digit code.....

OK, on my board it is the one near my sound chip so it should be the same for you.

They are zeros. That is the one.

which is also 12 digits!!!! :))) what do we do? :) I wrote that down too, that one is larger fonts I can tell the numbers fine on that one

5xxxxxxxxx

I edited out the numbers in your post, hackers can do a lot with your Mac address 

I am not familiar with thunderbolt add in cards but I would imagine it shouldn't be much different to any other add in card with regards to drivers and compatibility. 

after getting into windows 10 it gave an error about repairing some drive errors... said I need to restart it, I am doing that right now I wonder what now

this one is the AsRock Thunderbolt 2 AIC that I have, now I plugged off everything, to insert it back up again, and will restart it I did correct research to make sure the PCIE 2 is the one I install it as per its instructions (The Reason I didn't get a second GPU was to keep this PCIE slot open for Thunderbolt 2)

Oh and just an FYI, you should install dual GPUs in slots 1 and 3 as they are both x16. PCIe 2 is only wired as x4 which is probably why they recommend using it. PCIe 5 is x8. 

I haven't read the entire manual though so I am not sure if using certain slots may disable others, I doubt it though.

when i go to UEFI again on Tools/System Browser PCIE2 is still coming up Empty! even thought the Thunderbolt is there and cables connected as per instructions on its manual

check this out so I was able to install the Thunderbolt driver as you can see above photo, however now I am checking in UEFI in System browser to see...

I assume you had no issues with steps 1 - 3

Did you connect the TBT Header Cable to the TBT Header (A) as instructed?

As far as I can tell the AIB won't detect if that step is missed.

Also, what position are the jumpers on the card set to? 1-2 or 2-3?

If you use the "print screen" key on your keyboard you can then open an image manipulation app (MS 

the Slot is Empty?! :)

here is a picture:

Do you have the "TBT Header Cable" connected to the TBT Header? It is the header above the yellow highlighted COM port in your image.  

I doubt you would have damaged anything by not doing this but it is good practice which is why I mentioned it 

Trying the other jumper position is worth a shot but I suspect it won't make a difference. If that fails see if you can get the card to detect in PCIe slot 5, the one nearest the TBT header.

Don't bother trying slot 5, the card is meant to get it's PCIe lanes from the PCH (chipset) and slot 2 is the only slot that gets it's PCIe lanes from the chipset. 

Let's assume there is a problem with the thunderbolt card, or I can't just make it work, is it possible there is something wrong with the motherboard of PCIE2 slot, is there a way to test that slot some other way and then focus on getting the Thunderbolt work?

Have you tried installing the http://www.asrock.com/mb/spec/card.asp?Model=Thunderbolt%202%20AIC&cat=Download" rel="nofollow - TBT software and connecting a TBT device to see if it detects?

so I assume you want me to choose Gen2?

I am trying that now, with jumpers being 1-2