Hi all,
I have been a long time reader (lurker) here and in other related fora - and have spent enormous amount of time on a very similar project inspired by this thread: ASRock x99e-itx/ac + 2x GTX1080's (butchered into single-slot cards and crammed in an NCase with the EKWB Predator 240 All-In-One solution to watercool everything and the SIlverstone 700W SFX-L PSU for power).
I have used Amerirack's ARC1-PERY423-C10, which is described as 402/C10, PCIe x16 splitter, one PCIe x16 to dual PCIe 16(x8 electric) reversed flexible riser/splitter w/10cm ribbon, RoHS, 3.0 Gen3 compatible and can even be screwed on the NCase right next to the mini-ITX m/b.
(link: ARC1-PELY423-C7V3) In other words perfect for this build. So far so good, except I have EXACTLY the same instability issues described above in the 2x Nano's setup!
Both cards are recognised in WIndows Device Manager but unless I disable one of them (by right-click disable) , if I try to use them both the machine will eventually (very quickly) lock-up, the cursor will freeze and only a hard reset restores things. In fact I think the display driver hangs but the rest of the OS underneath works normally, I can remote-login etc. I have tried endless combinations of Windows versions, nVidia driver versions etc but always same story - cursor freeze that "feels" like a hardware issue.
ASRock technical support have proven extremely helpful with multiple beta bios versions to make things work (Broadwell+bifurcation is broken in current public bioses, at least for my particular setup so they came back with a custom one) and I am still iterating with them trying to nail things down. If I get anywhere I will post here - I even started a case at nVidia blaming the drivers. Otherwise "interference" or the 75w limit per PCIe slot or who knows..
Also working with the same board and splitter, definitely post back if you get things working! Is the custom BIOS you're working with available in the beta section on the ASRock site? How is it different from the public ones that have bifurcation support?