This raises my eyebrow (left).
The RTX 4090 is a PCIe Gen 4 device. Gen 4 is not known to be cable-friendly without intervention (e.g., a retimer) and especially if you’re hanging the cables off slots that far down.
If your cables must be that long, try taking the slot down a notch to Gen 3 speeds.
If the performance penalty is too great, consider a retimer, Slim SAS cable, and PCIe slot adapter chain.
There’s also this massive thread for general problems including the one such as yours: https://forum.level1techs.com/t/a-neverending-story-pcie-3-0-4-0-5-0-bifurcation-adapters-switches-hbas-cables-nvme-backplanes-risers-extensions-the-good-the-bad-the-ugly