so they are placed in slots PCIe3.0_1 and 3 now? or rather 2B and you meant 2A as being too close?
per manual those are slot names:
red PCIe_1 (16x if single or 8x native)
(empty space)
red PCIe_2A (16x switched)
black PCIe_2B (8x native)
red PCIe_3 (8x switched)
black short pcie x4
red PCIe_4 (8x switched)
are you sing a flexible 2-way bridge now? not saying this is an issue, no not at all, but I have an idea since no other devices are present. move the secondary card further down and connect those 2 using a solid 3-way SLI bridge. the secondary will then run through synthetic (multiplexed via PLX chip) 8x while primary in top slot will stay on native 8x, but it should work still without trouble. wondering if your slot 2B (native 8x) work fine ... or maybe (if cards are functional fully, confirmed by swapping them around) the BIOS is quirky about them both at once ...
... but first make sure the secondary is fully seated and coming loose after a while.
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