I apologize if the topic of my inquiry is not relevant to the subject matter of the forum but I really could use some expert help. The issue is in regards to a bios mod that i made that bifurcated my last pcie port on the motherboard into two separate pairs of lanes. The motherboard is an Msi X99a motherboard with a 6850k cpu. The mod altered address 0x539 inside of the IntelRcSetup module setting it to 0x0 which caused the IOU 8X integrated IO controller to split into two. Usually you have four controllers DMI at 4 lanes, IOU1 at 8X, IOU2 16X, and IOU3 also at 16X.
After successfully bifurcating the 8X port I installed a Plextor M8Pey Nvme 4x pcie card in the 8x slot and a Samsung 950 Pro nvme drive in the onboard M.2 connector. I also used a Supermicro bifurcated 8X to 4X4X adapter riser card to allow the Plextor Nvme to operate using the 2nd 4X lane pairs off of the motherboard while at the same time the M.2 is set to Pci-e operation. This worked great at first until I noticed that randomly the Plextor drive would sometimes initialize its negotiated link speed at 2.5 GT/s as opposed to 8.0 GT/s. This shifting was random.
In matter of fact I found that reinstalling the Nvme driver would force 8.0 GT/s operation at reboot every time. So it makes me think that there must be setpci setting to fix it at 8.0 gt/s mode but i have no idea how to fix this. I should note this is in Windows 10 64. I am verifying my link speed with HWinfo and Siv64. Also I verified that the link speed issue was a direct result of the mod and not related to the riser card, and goes away when I undo the mod. My theory is much like how my video cards shift the link speed from 2.5 to 8 gt/s I am hopeful for a software solution.
If anyone can make any suggestions i would appreciate it,