diff --git a/GPU/Common/PresentationCommon.cpp b/GPU/Common/PresentationCommon.cpp
index 8d71a9e92c..69e440a64c 100644
--- a/GPU/Common/PresentationCommon.cpp
+++ b/GPU/Common/PresentationCommon.cpp
@@ -801,6 +801,7 @@ void PresentationCommon::CopyToOutput(OutputFlags flags, int uvRotation, float u
 	if (usePostShader) {
 		// When we render to temp framebuffers during post, we switch position, not UV.
 		// The flipping here is only because D3D has a clip coordinate system that doesn't match their screen coordinate system.
+		// The flipping here is only because D3D has a clip coordinate system that doesn't match their screen coordinate system.
 		bool flipped = flags & OutputFlags::POSITION_FLIPPED;
 		float y0 = flipped ? 1.0f : -1.0f;
 		float y1 = flipped ? -1.0f : 1.0f;
diff --git a/UI/EmuScreen.cpp b/UI/EmuScreen.cpp
index ac3beecd3b..c2c420c15b 100644
--- a/UI/EmuScreen.cpp
+++ b/UI/EmuScreen.cpp
@@ -1326,7 +1326,7 @@ ScreenRenderFlags EmuScreen::render(ScreenRenderMode mode) {
 		// We only bind it in FramebufferManager::CopyDisplayToOutput (unless non-buffered)...
 		// We do, however, start the frame in other ways.
 
-		if ((g_Config.bSkipBufferEffects && !g_Config.bSoftwareRendering) || Core_IsStepping()) {
+		if ((skipBufferEffects && !g_Config.bSoftwareRendering) || Core_IsStepping()) {
 			// We need to clear here already so that drawing during the frame is done on a clean slate.
 			if (Core_IsStepping() && gpuStats.numFlips != 0) {
 				draw->BindFramebufferAsRenderTarget(nullptr, { RPAction::KEEP, RPAction::CLEAR, RPAction::CLEAR }, "EmuScreen_BackBuffer");
@@ -1348,12 +1348,12 @@ ScreenRenderFlags EmuScreen::render(ScreenRenderMode mode) {
 		System_Notify(SystemNotification::KEEP_SCREEN_AWAKE);
 	} else if (!Core_ShouldRunBehind() && strcmp(screenManager()->topScreen()->tag(), "DevMenu") != 0) {
 		// Just to make sure.
-		if (PSP_IsInited() && !g_Config.bSkipBufferEffects) {
+		if (PSP_IsInited() && !skipBufferEffects) {
 			PSP_BeginHostFrame();
 			gpu->CopyDisplayToOutput(true);
 			PSP_EndHostFrame();
 		}
-		if (!gpu->PresentedThisFrame()) {
+		if (!framebufferBound && !gpu->PresentedThisFrame()) {
 			draw->BindFramebufferAsRenderTarget(nullptr, { RPAction::CLEAR, RPAction::CLEAR, RPAction::CLEAR, }, "EmuScreen_Behind");
 		}
 		// Need to make sure the UI texture is available, for "darken".
diff --git a/UI/NativeApp.cpp b/UI/NativeApp.cpp
index 38e1e60b7d..89ce32f92f 100644
--- a/UI/NativeApp.cpp
+++ b/UI/NativeApp.cpp
@@ -1061,23 +1061,6 @@ void NativeFrame(GraphicsContext *graphicsContext) {
 	ProcessWheelRelease(NKCODE_EXT_MOUSEWHEEL_UP, startTime, false);
 	ProcessWheelRelease(NKCODE_EXT_MOUSEWHEEL_DOWN, startTime, false);
 
-	std::vector<PendingMessage> toProcess;
-	{
-		std::lock_guard<std::mutex> lock(pendingMutex);
-		toProcess = std::move(pendingMessages);
-		pendingMessages.clear();
-	}
-
-	for (const auto &item : toProcess) {
-		if (HandleGlobalMessage(item.message, item.value)) {
-			// TODO: Add a to-string thingy.
-			INFO_LOG(SYSTEM, "Handled global message: %d / %s", (int)item.message, item.value.c_str());
-		}
-		g_screenManager->sendMessage(item.message, item.value.c_str());
-	}
-
-	g_requestManager.ProcessRequests();
-
 	// it's ok to call this redundantly with DoFrame from EmuScreen
 	Achievements::Idle();
 
@@ -1104,6 +1087,24 @@ void NativeFrame(GraphicsContext *graphicsContext) {
 
 	g_screenManager->update();
 
+	// Do this after g_screenManager.update() so we can receive setting changes before rendering.
+	std::vector<PendingMessage> toProcess;
+	{
+		std::lock_guard<std::mutex> lock(pendingMutex);
+		toProcess = std::move(pendingMessages);
+		pendingMessages.clear();
+	}
+
+	for (const auto &item : toProcess) {
+		if (HandleGlobalMessage(item.message, item.value)) {
+			// TODO: Add a to-string thingy.
+			INFO_LOG(SYSTEM, "Handled global message: %d / %s", (int)item.message, item.value.c_str());
+		}
+		g_screenManager->sendMessage(item.message, item.value.c_str());
+	}
+
+	g_requestManager.ProcessRequests();
+
 	// Apply the UIContext bounds as a 2D transformation matrix.
 	// TODO: This should be moved into the draw context...
 	Matrix4x4 ortho = ComputeOrthoMatrix(g_display.dp_xres, g_display.dp_yres);