I am having a problem where my GPU will only establish a PCIe link of x1 4.0 on cold boots and after resuming from sleep. It will work normally at x16 4.0 on restart. I believe this to be a BIOS or hardware issue as I have tried to eliminate software causes by doing a repair install of Windows and removing drivers with DDU and re-installing.

My motherboard and GPU manufacturer refuse to even attempt troubleshooting because I am running a Windows beta build.

When is PCIe link training done? Could Windows cause a problem with establishing PCIe links? It's my understanding that this is all done at the hardware level before the OS is loaded.

Edit: Also I noticed this behavior started after a BIOS update, But it may have been happening prior to that and I didn't notice.

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Edit: for anyone wondering, rolling back the BIOS resolved the issue.