Thank you for your answers, Jason and Alberto.
While it's true that the hypercard is a PCIe 3.0 device, I did not see the reason yet why it would not operate in a PCIe 2.0 slot with lower throughput. And I am not sure but - is Intel VROC required to use all four M.2 slots?
Anyways, I am happy to report that I "resolved" the issue partially by getting rid of the GPU that occupies two slots, replacing it by one that occupies just 1 slot. Then I installed the USB3 controller card next to it, resulting in the following setup:
1. (MIO): empty 2. GPU 3. USB3 controller card 4. Hypercard 5. Empty
This way, I have graphics, USB 3.0 and two M.2 slots working. In addition, I noticed that the system (without usb3) takes around 7-8W less in idle than with the previous gpu installed. That's a bit surprising as the old gpu was advertised to use only ~5.5W total while idle (but I wondered while it gets so hot, I thought this was due to it being installed so close to CPU0's huge heatsink). As I don't need that much GPU power anyways, the swap had at least a nice (unexpected) side-effect for me.
However, the fact that I still can use only two M.2 cards is somewhat disappointing. Since there are also other vendors of comparable PCIe quad-M.2 cards, I welcome any reports (both positive and negative) from people who tried different m.2 quad card models in a KGPE-D16.
Cheers, Daniel
Did you get my email? can you provide a: dmesg # lspci -t -v # lspci -vv
Thanks
Most quad adapters use PCI-e bifurcation not a PCI-e switch and AFAIK not many boards support bifurcation so you would need a switched model which you might have (I am not sure) if you do have a switched card I would also contact the OEM as there shouldn't be any reason as to why it doesn't work.
Not having PCI-e 3.0 wouldn't make a difference at all in terms of the card working with all 4 cards and if the cards uplink is PCI-e 2.0 x8 or x16 you won't notice a difference in speed.
VROC is an optional wintel gimmick addon that shouldn't be required for it to work - if you could link a .pdf manual I will find out if it is switched or bifurcated.
Forgot to say - a theory is that the issue may be that you lack enough lanes in the slot you are using. As ASUS was cheap they didn't add a second northbridge to obtain more PCI-e lanes as was done with the TYAN boards so while the slots are x16 physical you can't run all of them at that all the time - I would consult the manual to see which is which I believe the configurations are either x16 x8 x8 x4 or x16 x16 x4 (both also can use the PIKE slot which part of it is a reversed PCI-e slot connected to the southbridge rather than the northbridge)
Using an x8 slot with bifurcation and 4 x4 M2 cards could mean that you lack enough lanes to bifurcate all 4 - as an experiment I suggest hooking up the card to an x16 configured slot and putting your GPU in the x8 slot instead (you won't notice a difference)
As you are able to hook up two M2 cards it appears that bifurcation is working as I don't see any information that indicates you having a switched card.
I suggest emailing my directly via your other email account as I am moderated on the coreboot ML so replies take a long time - also I don't like emailing gmail addresses.