I'm not sure what WinOF version you have installed but assuming it is WinOF v5.35_FUR - then VM (Win2012R2) should have no problem picking up a VF of a preconfigured SR-IOV ETH on the top of a Win2016 Hyper-v
Suggesting to ensure::
1. Both Hyper-V & VMs have the same winof driver version (depending on the OS type)
2. the CX-3 Pro adapter has the latest FW bunt (as per adapter's PSID)
for more posible VMs restrictions - read "known-issues" in the release-note of winof v5.35
I have the latest version of WinOF installed. Also, I notice that my vm's are unstable when SR-IOV is enabled. Does SR-IOV need to be supported at the BIOS level? I have a S5520HC motherboard which is dated and I can't find any info to see if SR-IOV is supported on that board. I've read that it's part of the pci spec and so assumed it's a standard feature, but I've also seen postings that suggest it needs BIOS support.