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Thunderbolt card install in z170-a

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Hey, guys. I'm not sure if this belongs in the hardware or bios sections, since its kinda both.

System:
OS 10.12
Asus Z170-A
i5 6600k
Asus GTX-1070
Asus Thunderbolt EXII
2x Crucial SSD (one for win, one for osx)
boot order is osx first so we can choose windows from clover

So first off, our plan was to use the onboard graphics for osx, since the 10 series isn't supported. The end goal is to use the windows side for gaming, and the mac side for music production (with a thunderbolt audio interface).

The install went smoothly, and the graphics switching has been working fine, until we tried installing the thunderbolt card (about a week after the initial install). Installed the card in pcie x16_3, went to bios and enabled thunderbolt and booted into windows, which detected it like a champ. In osx, nothing. When we tried setting the slot to x4 (default is x2), osx wouldn't boot. It actually kinda crashed our whole rig, clover started displaying in text (looked like the old windows safe mode screen), then it wouldn't boot at all and we couldn't get into bios. After pulling the mobo battery, we tried a few other settings which didn't work. We also tried putting it in the 2nd pcie slot, since the 3rd shares some bandwidth with sata and usb etc. That hasn't worked either.

We have gotten osx to see the device one time. We booted osx (sys profiler didn't show any thunderbolt hardware), then we plugged the interface in and rebooted. That seemed to work, although we were getting a ton of noise through our speakers (through the interface), and when we tried to do it again, it wouldn't boot into osx at all.

Another thing we've just discovered is that turning thunderbolt on in bios breaks the onboard graphics. Up till now we were using the graphics card in standard upnp make it work mode.

Its a hard one to find info on, most threads talking about thunderbolt cards are talking about z97/x99 etc, and even then there isn't really a consensus on how to get these things to work. Any help or ideas shall be bountifully rewarded in the form of my undying gratitude and well wishes.
 
I've posted pretty extensively on how to get my ASUS ThunderboltEX-II DUAL card working. Initially it was only working in the little X4 slot, but I've now got it working in the full-sized slot furthest away from the CPU. There are several settings in the TB BIOS menu that you need to be aware of. One is that you must set it to "Legacy" mode. The other has to do with telling the BIOS where the TB card is plugged in. There are 2 drop-down menus about 1/3 of the way down. It escapes me what they are called, as I'm away from home & can't check. But those 2 drop-downs work in concert & that's how you get it to map to the PCIEX16_5. Also make sure you disable wake from TB sleep, as well as any other things like boot from TB USB, etc.

Then you need to actually install Windows & install the Windows firmware/drivers to get it activated. I didn't see anything specific about what you did under Windows. Again, I've posted extensively about this phase of the process (including screen shots). I'd share some links, but I'm on my work laptop and don't have those bookmarks handy.

The same card works on ASUS Z97, Z170, and X99 series boards (the ones where TB is supported with the mobo header for the little jumper cable). So the process to get it activated is identical, regardless of which board you have.
 
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