I appologize. I think I said that wrong earlier. I believe it is x16 1.1 to 2.0 or 2.0 to 3.0 where the change happens under load. One of the two anyhow. Regardless, it could be something else. Have you tried disconnecting all other drives except the OS drive to see if it's a lane issue? I'm assuming your graphics card IS installed in the primary x16 slot, closest to the CPU socket?
I would do ALL of the following, FIRST, to see if there is any change. Also, knowing your full hardware specs including the EXACT power supply model would be helpful. Insufficient power delivery could be at play as well. I've seen a poor quality power supply cause lane fluctuations before. Not often, and not consistently, but I've seen it.
Here are the first steps to take when trying to solve these kinds of hardware problems. If you have already tried these steps, all of them, exactly as outlined, we can move along to more advanced solutions.
If there are any you have NOT done, it would be advisable to do so if for no other reason than to be able to say you've already done it and eliminate that possibility.
First, make sure your motherboard has the MOST recent BIOS version installed. If it does not, then update. This solves a high number of issues even in cases where the release that is newer than yours makes no mention of improving graphics card or other hardware compatibility. They do not list every change they have made when they post a new BIOS release.
Second, go to the product page for your motherboard on the manufacturer website. Download and install the latest driver versions for the chipset, storage controllers, audio and network adapters. Do not skip installing a newer driver just because you think it is not relevant to the problem you are having. The drivers for one device can often affect ALL other devices and a questionable driver release can cause instability in the OS itself. They don't release new drivers just for fun. If there is a new driver release for a component, there is a good reason for it. The same goes for BIOS updates.
IF you have other hardware installed or attached to the system that are not a part of the systems covered by the motherboard drivers, then go to the support page for THAT component and check to see if there are newer drivers available for that as well. If there are, install them.
The last thing we want to look at, for now anyhow, is the graphics card drivers. Regardless of whether you "already installed the newest drivers" for your graphics card or not, it is OFTEN a good idea to do a CLEAN install of the graphics card drivers. Just installing over the old drivers OR trying to use what Nvidia and AMD consider a clean install is not good enough and does not usually give the same result as using the Display Driver Uninstaller utility. This has a very high success rate and is always worth a shot.
If you have had both Nvidia and AMD cards installed at any point on that operating system then you will want to run the DDU twice. Once for the old card drivers (ie, Nvidia or AMD) and again for the currently installed graphics card drivers (ie, AMD or Nvidia). So if you had an Nvidia card at some point in the past, run it first for Nvidia and then after that is complete, run it again for AMD if you currently have an AMD card installed.
Here are the full instructions on running the Display driver uninstaller and CLEAN installing new drivers.