You are having a problem when you plug this card into the x4 connector (A)? Have you tried the x8 connector (C)? What about the x1 connectors? Two of them (D and especially I) should be available with a conventional graphics card installed (in F). If your cooling solution is making the first x1 slot unavailable (I), there is something wrong with this solution (or its alignment). Perhaps you should include a picture so we can see what is going on.
Intel exited the Desktop Boards business a number of years ago. All boards are now well beyond their end-of-life and end-of-interactive-support dates. Quite simply, there are no BIOS resources available to look into an issue such as this. You will just have to figure out a way to make it work; there's nothing you can do in the BIOS configuration regarding an issue like this. I am unaware of any issues that would result in the board hanging if this card is properly meeting the PCIe requirements.
Sorry, but this is the reality of the situation,
On my KLT, referencing the tech spec page 13, section 1.1.2, (https://www.intel.com/content/dam/support/us/en/documents/motherboards/desktop/dz87klt-75k/dz87klt-7... https://www.intel.com/content/dam/support/us/en/documents/motherboards/desktop/dz87klt-75k/dz87klt-7...… ) I have the following in use.
X1 slot I - sound card
x16 slot F - wide video card (covers X1 slot E)
X1 slot D - modem
Slots C, B, and A are open and usable.
All works as it should.
It works fine on 1x slot but why on earth design a board and block 2 slots of 1x with a proper graphics card. The ancient PCI should have been there as if the board is needed for something ancient there is no need for the dedicated graphic card.
My point is that this configuration works perfectly fine with any half decent Asus motherboard starting from 2nd generation - Sandy Bridge. I've only recently upgraded to Haswell from Sandy Bridge as I see no point of spending my hard earned money on a brand new system with mega expensive ram, and don't see even a double performance increase...
The sound card is Asus Xonar Phoebus and it does indeed comply with 1x specifications and work just fine in a 1x slot however it must also work in any of the 16x pci-e slots as these slots are not just dedicated for the graphics only, it's not agp at the end of the day. The problem is that the motherboard or a bios or whatever even controls the PCI lanes, sees the sound card as a graphics card and gives me a graphic card fault and won't boot...
I have a Noctua cooler and happy with that, it's that big that it covers all the ram slots as well, but that doesn't bother me much.
My current solution is to put my graphics card in to a second 16x pci-e slot only to get the 8x speed and to stick the sound card on top. But this is wrong, may be something can be adjusted in the bios so it t won't treat the sound card as a graphics card?
Not sure what end of life you're talking about, I've just updated the bios to 2018 version - ) and it's not like my i7 with 32gb ram will have any issues to run Windows 10 for the next 5 years...
The KLT board is 5 years old. The bios was updated 3 years ago (0457). The bios update to which you are referring in 2018 (0458) was only done to address SA-00088.
So, unless you purchased the KLT board used, you knew the [slot] configuration 5 years ago.
https://ark.intel.com/products/70898/Intel-Desktop-Board-DZ87KLT-75K Intel® Desktop Board DZ87KLT-75K Product Specifications
The KLT is a very fine board. If I can find another in good condition, I will purchase it. That the KLT does not meet your needs is unfortunate. As I detailed in my slot usage, the KLT is quite configurable. However, I selected my board based on my needs and add-ons before purchasing.
There will be no more updates for the bios, unless there is another security issue that needs to be addressed at that level. So, perhaps your solutions is in using another manufacturers board.
I will add that I do not understand why the board is not working in either the x8 or x4 slots (you did try it in the x8, right?). We could speculate all day regarding physical slot alignment issues, BIOS issues, etc. and etc., but that's a waste of time. As I said earlier, most graphics cards only cover two slots. What card do you have that it is covering three slots? Does the Noctua solution really cover up the x1 slot between the x16 slot and the processor socket? I have seen lots of cooling solutions that take up room north/south of the processor socket, but not (that far) east/west.
Since this board is long past its EOL and EOS dates, there is no recourse for replacement or repair and no resources available to diagnose this further. As Al says, either you use it as-is or you trash it. If you are going to trash it, I know a few good homes willing to take it off your hands...