diff --git a/src/AutoPilotPlugins/AutoPilotPluginManager.cc b/src/AutoPilotPlugins/AutoPilotPluginManager.cc
index 8017253..e164470 100644
--- a/src/AutoPilotPlugins/AutoPilotPluginManager.cc
+++ b/src/AutoPilotPlugins/AutoPilotPluginManager.cc
@@ -28,6 +28,7 @@
 #include "PX4/PX4AutoPilotPlugin.h"
 #include "Generic/GenericAutoPilotPlugin.h"
 #include "QGCApplication.h"
+#include "QGCMessageBox.h"
 #include "UASManager.h"
 
 IMPLEMENT_QGC_SINGLETON(AutoPilotPluginManager, AutoPilotPluginManager)
@@ -81,6 +82,9 @@ void AutoPilotPluginManager::_uasCreated(UASInterface* uas)
             plugin = new GenericAutoPilotPlugin(uas, this);
             Q_CHECK_PTR(plugin);
             _pluginMap[MAV_AUTOPILOT_GENERIC][uasId] = QSharedPointer<AutoPilotPlugin>(plugin);
+            QGCMessageBox::warning("Partial Support AutoPilot",
+                                   "Warning: You have connected QGroundControl to a firmware flight stack which is only partially supported. "
+                                   "If you are using the APM Flight Stack it is currently recommended to use Mission Planner, APM Planner or Tower as your ground control station.");
     }
 }
 
diff --git a/src/FactSystem/FactSystemTestBase.cc b/src/FactSystem/FactSystemTestBase.cc
index cd6a643..5650f70 100644
--- a/src/FactSystem/FactSystemTestBase.cc
+++ b/src/FactSystem/FactSystemTestBase.cc
@@ -30,6 +30,7 @@
 #include "AutoPilotPluginManager.h"
 #include "UASManager.h"
 #include "QGCApplication.h"
+#include "QGCMessageBox.h"
 #include "QGCQuickWidget.h"
 
 #include <QQuickItem>
@@ -49,6 +50,11 @@ void FactSystemTestBase::_init(MAV_AUTOPILOT autopilot)
     MockLink* link = new MockLink();
     link->setAutopilotType(autopilot);
     _linkMgr->_addLink(link);
+    
+    if (autopilot == MAV_AUTOPILOT_ARDUPILOTMEGA) {
+        // Connect will pop a warning dialog
+        setExpectedMessageBox(QGCMessageBox::Ok);
+    }
     _linkMgr->connectLink(link);
     
     // Wait for the uas to work it's way through the various threads
@@ -56,6 +62,10 @@ void FactSystemTestBase::_init(MAV_AUTOPILOT autopilot)
     QSignalSpy spyUas(UASManager::instance(), SIGNAL(activeUASSet(UASInterface*)));
     QCOMPARE(spyUas.wait(5000), true);
     
+    if (autopilot == MAV_AUTOPILOT_ARDUPILOTMEGA) {
+        checkExpectedMessageBox();
+    }
+    
     _uas = UASManager::instance()->getActiveUAS();
     Q_ASSERT(_uas);
     
diff --git a/src/qgcunittest/MainWindowTest.cc b/src/qgcunittest/MainWindowTest.cc
index 12cabaa..363bc2e 100644
--- a/src/qgcunittest/MainWindowTest.cc
+++ b/src/qgcunittest/MainWindowTest.cc
@@ -67,6 +67,11 @@ void MainWindowTest::_connectWindowClose_test(MAV_AUTOPILOT autopilot)
     Q_CHECK_PTR(link);
     link->setAutopilotType(autopilot);
     LinkManager::instance()->_addLink(link);
+    
+    if (autopilot == MAV_AUTOPILOT_ARDUPILOTMEGA) {
+        // Connect will pop a warning dialog
+        setExpectedMessageBox(QGCMessageBox::Ok);
+    }
     linkMgr->connectLink(link);
     
     // Wait for the uas to work it's way through the various threads
@@ -74,6 +79,10 @@ void MainWindowTest::_connectWindowClose_test(MAV_AUTOPILOT autopilot)
     QSignalSpy spyUas(UASManager::instance(), SIGNAL(activeUASSet(UASInterface*)));
     QCOMPARE(spyUas.wait(5000), true);
     
+    if (autopilot == MAV_AUTOPILOT_ARDUPILOTMEGA) {
+        checkExpectedMessageBox();
+    }
+    
     // Cycle through all the top level views
     
     _mainToolBar->onSetupView();