I am trying to split two separate video cards up on my MSI Z77A-GD65 motherboard, and when they're in the top and middle x16 ports, they both end up in the same IOMMU group with the PCIe root controller. I've tried ACS override, but that just results in outright failure when attempting to bind either card.

do you have any other ports on the board you could try?

In my current case configuration, I cannot test any other x16 ports, as the bottom slot is blocked to a single slot by my current case.

 

I have decided to give up on importing two separate video cards into separate VMs at this time, and will consider using those two slots with the one Windows 10 VM in the future, if I ever get more than one identical video card for the purpose.

 

The problem was that the two slots share an IOMMU group with the PCIe root node, so they cannot be broken up without ACS overrides, and even with overrides, each individual video card slot still needs the one root node.

You could try and use the blocked slot by using one of these 

http://www.ebay.co.uk/itm/New-PCI-Express-PCI-E-16X-Riser-rd-Ribbon-Extender-Extension-20cm-ble-/222114770424?hash=item33b7126df8:g:EFUAAOSwZ1BXfmPQ

 

https://www.amazon.com/Express-Riser-Extender-Flexible-Extension/dp/B008BZBFTG

 

I may try that if I'm desperate to find if the slot works for a separate PCIe root, but it wouldn't be a permanent solution, as this case has absolutely nowhere else to put a video card, especially not a full length one like this.

Bumping with a report that I found the "cause" of my problem. It's purely down to trying to use multiple virtual machines on a non-ACS configuration. I need either a Core Extreme or Xeon board and processor to have full ACS support, which would allow splitting up PCIe roots and GPUs in adjacent slots.

 

I'll consider that next time I'm in the market to buy a new motherboard and processor, and likely also memory.