Since you are using the Hyte Y70, your GPU is vertically mounted using a PCIe riser cable. Riser cables are notorious for causing exactly what you are describing. A cold system might have slight physical contraction that affects the pins, or the motherboard might be failing to negotiate the PCIe 5.0/4.0 link speed on a cold boot.
The Fix: Pull the motherboard out of the case (or carefully re-orient things) and plug the RTX 5090 directly into the motherboard’s top PCIe slot, bypassing the riser cable entirely. If the issue disappears, your Hyte riser cable is faulty or struggling with the 5090's bandwidth.
Temporary Bios Tweak: Go into your MSI BIOS and manually change the PCIe slot configuration from "Auto" or "Gen 5" to "Gen 4". This reduces signaling strain and often fixes riser issues.