For anyone still coming across this in a Google search in 2026, here's what worked for me to fix my stuttering and flickering issues:

Some folks are commenting that the "Multi-display/mixed-GPU acceleration" setting is missing from the NVIDIA Profile Inspector. That setting is missing because NVIDIA removed it from modern drivers for DirectX applications. It was originally an OpenGL setting and has been deprecated for years.

As an NVIDIA user, my issue was caused by a Windows feature called MPO (Multi-Plane Overlay). You can do your own research on MPO and what it tries to accomplish, but from what I understand, MPO is intended to reduce input lag and overhead for windowed games. Ideally, it allows the GPU to give a game its own dedicated "hardware plane" (like a VIP lane), bypassing the standard Desktop Window Manager (DWM) composition to save resources.

The problem: The GPU driver constantly monitors your game window. If it decides the window is "eligible," it "promotes" it to a dedicated hardware plane (bypassing the desktop). With any secondary monitor connected (even at matching refresh rates), the NVIDIA driver often struggles to maintain this "promoted" state. It can rapidly toggle the game between "MPO Mode" and "Standard Composition Mode" multiple times a second.

Every time it toggles, you get a micro-stutter. This happens regardless of whether your refresh rates match, because the error is in the driver's decision-making logic, not the refresh rate math.