diff --git a/src/Core.cc b/src/Core.cc
index b49eed18eab00942c85dadd72ccfd89f98197b69..cf0f0c3d1433ed2ae4bda109f4152a6af318327b 100644
--- a/src/Core.cc
+++ b/src/Core.cc
@@ -91,6 +91,8 @@ Core::Core(int &argc, char* argv[]) : QApplication(argc, argv)
     //     "Warning: Do not use this function in conjunction with Qt Style Sheets."
     // setFont(fontDatabase.font(fontFamilyName, "Roman", 12));
 
+    mainWindow = MainWindow::instance();
+
     // Start the comm link manager
     splashScreen->showMessage(tr("Starting Communication Links"), Qt::AlignLeft | Qt::AlignBottom, QColor(62, 93, 141));
     startLinkManager();
@@ -106,6 +108,9 @@ Core::Core(int &argc, char* argv[]) : QApplication(argc, argv)
     splashScreen->showMessage(tr("Starting User Interface"), Qt::AlignLeft | Qt::AlignBottom, QColor(62, 93, 141));
     // Start UI
 
+        // Remove splash screen
+    splashScreen->finish(mainWindow);
+
     // Connect links
     // to make sure that all components are initialized when the
     // first messages arrive
@@ -125,11 +130,6 @@ Core::Core(int &argc, char* argv[]) : QApplication(argc, argv)
     simulationLink->disconnect();
     //mainWindow->addLink(simulationLink);
 
-    mainWindow = MainWindow::instance();
-
-    // Remove splash screen
-    splashScreen->finish(mainWindow);
-
     // Check if link could be connected
     if (!udpLink->connect())
     {
diff --git a/src/comm/MAVLinkProtocol.cc b/src/comm/MAVLinkProtocol.cc
index 38e280aac86b8ebcfa9d36f7ea5aaf1a290e1aa0..dad9d91d1d6397574ad720f99dc8f9c97b0d676e 100644
--- a/src/comm/MAVLinkProtocol.cc
+++ b/src/comm/MAVLinkProtocol.cc
@@ -59,7 +59,8 @@ MAVLinkProtocol::MAVLinkProtocol() :
         heartbeatRate(MAVLINK_HEARTBEAT_DEFAULT_RATE),
         m_heartbeatsEnabled(false),
         m_loggingEnabled(false),
-        m_logfile(NULL)
+        m_logfile(NULL),
+        versionMismatchIgnore(false)
 {
     start(QThread::LowPriority);
     // Start heartbeat timer, emitting a heartbeat at the configured rate
@@ -91,7 +92,6 @@ MAVLinkProtocol::~MAVLinkProtocol()
 
 void MAVLinkProtocol::run()
 {
-
 }
 
 QString MAVLinkProtocol::getLogfileName()
@@ -146,7 +146,7 @@ void MAVLinkProtocol::receiveBytes(LinkInterface* link, QByteArray b)
                 // Check if the UAS has the same id like this system
                 if (message.sysid == getSystemId())
                 {
-                    qDebug() << "WARNING\nWARNING\nWARNING\nWARNING\nWARNING\nWARNING\nWARNING\n\n RECEIVED MESSAGE FROM THIS SYSTEM WITH ID" << message.msgid << "FROM COMPONENT" << message.compid;
+                    emit protocolStatusMessage(tr("SYSTEM ID CONFLICT!"), tr("Warning: A second system is using the same system id (%1)").arg(getSystemId()));
                 }
 
                 // Create a new UAS based on the heartbeat received
@@ -164,9 +164,12 @@ void MAVLinkProtocol::receiveBytes(LinkInterface* link, QByteArray b)
                 if (heartbeat.mavlink_version != MAVLINK_VERSION)
                 {
                     // Bring up dialog to inform user
-                    MainWindow::instance()->showCriticalMessage(tr("The MAVLink protocol version on the MAV and QGroundControl mismatch!"),
+                    if (!versionMismatchIgnore)
+                    {
+                        emit protocolStatusMessage(tr("The MAVLink protocol version on the MAV and QGroundControl mismatch!"),
                                                                  tr("It is unsafe to use different MAVLink versions. QGroundControl therefore refuses to connect to system %1, which sends MAVLink version %2 (QGroundControl uses version %3).").arg(message.sysid).arg(heartbeat.mavlink_version).arg(MAVLINK_VERSION));
-
+                        versionMismatchIgnore = true;
+                    }
 
                     // Ignore this message and continue gracefully
                     continue;
diff --git a/src/comm/MAVLinkProtocol.h b/src/comm/MAVLinkProtocol.h
index d3e436d34b6005f8adb19c3b48a4c8a27f6f9d5c..44ba9489de3b141aed1483c3ed5baf80f4fee11f 100644
--- a/src/comm/MAVLinkProtocol.h
+++ b/src/comm/MAVLinkProtocol.h
@@ -102,6 +102,7 @@ protected:
     int totalLossCounter;
     int currReceiveCounter;
     int currLossCounter;
+    bool versionMismatchIgnore;
 
 signals:
     /** @brief Message received and directly copied via signal */
@@ -110,6 +111,8 @@ signals:
     void heartbeatChanged(bool heartbeats);
     /** @brief Emitted if logging is started / stopped */
     void loggingChanged(bool enabled);
+    /** @brief Emitted if a message from the protocol should reach the user */
+    void protocolStatusMessage(const QString& title, const QString& message);
 };
 
 #endif // MAVLINKPROTOCOL_H_
diff --git a/src/ui/MainWindow.cc b/src/ui/MainWindow.cc
index a6d2da50172473486dc4da97edcb8604b5b39bba..968f64055963a065a533e12a0d5d37fa2100ef16 100644
--- a/src/ui/MainWindow.cc
+++ b/src/ui/MainWindow.cc
@@ -153,6 +153,7 @@ void MainWindow::buildCommonWidgets()
 {
     //TODO:  move protocol outside UI
     mavlink     = new MAVLinkProtocol();
+    connect(mavlink, SIGNAL(protocolStatusMessage(QString,QString)), this, SLOT(showCriticalMessage(QString,QString)), Qt::QueuedConnection);
 
     // Dock widgets
     if (!controlDockWidget)