I built an Intel system the other day for a friend (i5 13600k) on a MSI motherboard and I made sure to disable that in the BIOS, it's under the boot options in advanced - but it shouldn't have an impact after the initial boot. All it does is ask you, on boot, what software you want to install (MSI centre, drivers etc.)I've never heard of that, i'll check
Could you take things back to basics? Have you got other storage devices (SSD?) to hand that you could use? Remove both M.2s and just try it with an SSD to see what happens. Although saying that, it doesn't sound like it's an issue with the actual storage devices, they wouldn't create multiple instances of an application - surely that has to be CPU related?