A few things come to mind. First, would you check your motherboard specs to determine if the SSDs you are using are competing with the lanes to the GPU. Most people put the GPU in the first slot. Some motherboards share the lanes for that slot with the SSD controller. It would worth looking at to see if you are losing lanes to the GPU. That being said, I doubt that losing lanes to the GPU are what is causing this problem, but it deserves a look.
A few other things to consider. Do you have a spare cable to go between the GPU and the monitor? It could be you are having connectivity issues to the monitor, causing the game to drop to a lower frame rate, and you see the whole thing as stuttering. A cable swap would eliminate the cable. Another thing, less likely but worth asking, is what antivirus are you using? I have seen antivirus take control of files and folders for scanning, causing some slowdown but the slowdown would clear after the virus scanner was done. You might try using the exemptions option to omit the game folder or folders. Another factor to consider is a network latency issue. The first run of a game might look for some type of updates. If there are updates and they are slow to load, that might cause the game to lag. After the initial run the following runs would not exhibit the latency.
