Necro time.
So, I ran into this problem and I've been googling like crazy. I figured out the solution and implemented it and just wanted to share it for future googlers.
The problem is that if you have a non-full screen window that is positioned at 0,0 and covers all pixels of the screen windows will try to redirect the frame buffers for performance directly to the window. If a windows window has the flag WS_POPUP set while using this logic the screen will flickers when you focus and unfocus the window. The solution is to not set that flag, unfortunately this is buried deep in the lwjql code and I had to use the following semi hack to actually get to the windows window from the glfw window. If someone has a nicer looking solution, feel free to share

// in your application configuration, use config.setInitialVisible(false);
// in your create() method
@Override
public void create() {
preventFlickering();
....
}
private void preventFlickering() {
long hGLFWwindow = GLFW.glfwGetCurrentContext();
long hWnd = GLFWNativeWin32.glfwGetWin32Window(hGLFWwindow);
long style = User32.GetWindowLongPtr(hWnd, User32.GWL_STYLE);
style &= ~User32.WS_POPUP;
User32.SetWindowLongPtr(hWnd, User32.GWL_STYLE, style);
GLFW.glfwShowWindow(hGLFWwindow);
}