diff --git a/Core/Core.cpp b/Core/Core.cpp
index ecc13619c0..44b7f0c679 100644
--- a/Core/Core.cpp
+++ b/Core/Core.cpp
@@ -134,7 +134,9 @@ void UpdateScreenScale(int width, int height) {
 	NativeResized();
 }
 
-static inline void UpdateRunLoop() {
+void UpdateRunLoop() {
+	if (windowHidden)
+		return;
 	NativeUpdate(input_state);
 
 	{
@@ -149,12 +151,10 @@ static inline void UpdateRunLoop() {
 
 void Core_RunLoop() {
 	while ((GetUIState() != UISTATE_INGAME || !PSP_IsInited()) && GetUIState() != UISTATE_EXIT) {
-#if defined(USING_WIN_UI)
 		time_update();
+#if defined(USING_WIN_UI)
 		double startTime = time_now_d();
-		if (!windowHidden) {
-			UpdateRunLoop();
-		}
+		UpdateRunLoop();
 
 		// Simple throttling to not burn the GPU in the menu.
 		time_update();
@@ -166,7 +166,6 @@ void Core_RunLoop() {
 			GL_SwapBuffers();
 		}
 #else
-		time_update();
 		UpdateRunLoop();
 #endif
 	}
diff --git a/Core/Core.h b/Core/Core.h
index 2b10254d64..ba12a0a8c2 100644
--- a/Core/Core.h
+++ b/Core/Core.h
@@ -21,6 +21,7 @@
 #include "Core/CoreParameter.h"
 
 // called from emu thread
+void UpdateRunLoop();
 void Core_Run();
 void Core_Stop();
 void Core_ErrorPause();
diff --git a/Qt/mainwindow.h b/Qt/mainwindow.h
index bceb661a74..0bcd62e34b 100644
--- a/Qt/mainwindow.h
+++ b/Qt/mainwindow.h
@@ -39,6 +39,14 @@ public:
 	void updateMenus();
 
 protected:
+	void changeEvent(QEvent *e)
+	{
+		QMainWindow::changeEvent(e);
+		// Does not work on Linux for Qt5.2 or Qt5.3 (Qt bug)
+		if(e->type() == QEvent::WindowStateChange)
+			Core_NotifyWindowHidden(isMinimized());
+	}
+
 	void closeEvent(QCloseEvent *) { exitAct(); }
 
 signals:
diff --git a/native b/native
index e651601025..50d4319832 160000
--- a/native
+++ b/native
@@ -1 +1 @@
-Subproject commit e65160102599ddbce3410ec17f39364b93e22424
+Subproject commit 50d4319832447774c8eabb823e82c0898377419b