diff --git a/src/Vehicle/Vehicle.cc b/src/Vehicle/Vehicle.cc
index 4a33621ce2bee7ad941be7b84f815741238a4983..b01974e944d706edd860b9c169e6b867bf08bc12 100644
--- a/src/Vehicle/Vehicle.cc
+++ b/src/Vehicle/Vehicle.cc
@@ -488,6 +488,14 @@ void Vehicle::resetCounters()
 
 void Vehicle::_mavlinkMessageReceived(LinkInterface* link, mavlink_message_t message)
 {
+    // if the minimum supported version of MAVLink is already 2.0
+    // set our max proto version to it.
+    unsigned mavlinkVersion = _mavlink->getCurrentVersion();
+    if (_maxProtoVersion != mavlinkVersion && mavlinkVersion >= 200) {
+        _maxProtoVersion = _mavlink->getCurrentVersion();
+        qCDebug(VehicleLog) << "Vehicle::_mavlinkMessageReceived setting _maxProtoVersion" << _maxProtoVersion;
+    }
+
     if (message.sysid != _id && message.sysid != 0) {
         // We allow RADIO_STATUS messages which come from a link the vehicle is using to pass through and be handled
         if (!(message.msgid == MAVLINK_MSG_ID_RADIO_STATUS && _containsLink(link))) {
@@ -497,12 +505,6 @@ void Vehicle::_mavlinkMessageReceived(LinkInterface* link, mavlink_message_t mes
 
     if (!_containsLink(link)) {
         _addLink(link);
-
-        // if the minimum supported version of MAVLink is already 2.0
-        // set our max proto version to it.
-        if (_mavlink->getCurrentVersion() >= 200) {
-            _maxProtoVersion = _mavlink->getCurrentVersion();
-        }
     }
 
     //-- Check link status
@@ -839,6 +841,7 @@ void Vehicle::_setMaxProtoVersion(unsigned version) {
 
     // Set only once or if we need to reduce the max version
     if (_maxProtoVersion == 0 || version < _maxProtoVersion) {
+        qCDebug(VehicleLog) << "_setMaxProtoVersion before:after" << _maxProtoVersion << version;
         _maxProtoVersion = version;
         emit requestProtocolVersion(_maxProtoVersion);
 
@@ -873,60 +876,6 @@ void Vehicle::_handleHilActuatorControls(mavlink_message_t &message)
                                     hil.mode);
 }
 
-void Vehicle::_handleCommandAck(mavlink_message_t& message)
-{
-    bool showError = false;
-
-    mavlink_command_ack_t ack;
-    mavlink_msg_command_ack_decode(&message, &ack);
-
-    if (ack.command == MAV_CMD_REQUEST_AUTOPILOT_CAPABILITIES && ack.result != MAV_RESULT_ACCEPTED) {
-        // We aren't going to get a response back for capabilities, so stop waiting for it before we ask for mission items
-        qCDebug(VehicleLog) << "Vehicle failed to responded to MAV_CMD_REQUEST_AUTOPILOT_CAPABILITIES with error. Starting mission request.";
-        _setCapabilities(0);
-    }
-
-    if (ack.command == MAV_CMD_REQUEST_PROTOCOL_VERSION && ack.result != MAV_RESULT_ACCEPTED) {
-        // The autopilot does not understand the request and consequently is likely handling only
-        // MAVLink 1
-        if (_maxProtoVersion == 0) {
-            _setMaxProtoVersion(100);
-        }
-    }
-
-    if (_mavCommandQueue.count() && ack.command == _mavCommandQueue[0].command) {
-        _mavCommandAckTimer.stop();
-        showError = _mavCommandQueue[0].showError;
-        _mavCommandQueue.removeFirst();
-    }
-
-    emit mavCommandResult(_id, message.compid, ack.command, ack.result, false /* noResponsefromVehicle */);
-
-    if (showError) {
-        QString commandName = _toolbox->missionCommandTree()->friendlyName((MAV_CMD)ack.command);
-
-        switch (ack.result) {
-        case MAV_RESULT_TEMPORARILY_REJECTED:
-            qgcApp()->showMessage(tr("%1 command temporarily rejected").arg(commandName));
-            break;
-        case MAV_RESULT_DENIED:
-            qgcApp()->showMessage(tr("%1 command denied").arg(commandName));
-            break;
-        case MAV_RESULT_UNSUPPORTED:
-            qgcApp()->showMessage(tr("%1 command not supported").arg(commandName));
-            break;
-        case MAV_RESULT_FAILED:
-            qgcApp()->showMessage(tr("%1 command failed").arg(commandName));
-            break;
-        default:
-            // Do nothing
-            break;
-        }
-    }
-
-    _sendNextQueuedMavCommand();
-}
-
 void Vehicle::_handleCommandLong(mavlink_message_t& message)
 {
 #ifdef __ios__
@@ -2369,6 +2318,7 @@ void Vehicle::_sendMavCommandAgain(void)
     if (_mavCommandRetryCount++ > _mavCommandMaxRetryCount) {
         if (queuedCommand.command == MAV_CMD_REQUEST_AUTOPILOT_CAPABILITIES) {
             // We aren't going to get a response back for capabilities, so stop waiting for it before we ask for mission items
+            qCDebug(VehicleLog) << "Vehicle failed to responded to MAV_CMD_REQUEST_AUTOPILOT_CAPABILITIES. Setting no capabilities. Starting Plan request.";
             _setCapabilities(0);
             _startPlanRequest();
         }
@@ -2376,8 +2326,12 @@ void Vehicle::_sendMavCommandAgain(void)
         if (queuedCommand.command == MAV_CMD_REQUEST_PROTOCOL_VERSION) {
             // We aren't going to get a response back for the protocol version, so assume v1 is all we can do.
             // If the max protocol version is uninitialized, fall back to v1.
+            qCDebug(VehicleLog) << "Vehicle failed to responded to MAV_CMD_REQUEST_PROTOCOL_VERSION. Starting Plan request.";
             if (_maxProtoVersion == 0) {
+                qCDebug(VehicleLog) << "Setting _maxProtoVersion to 100 since not yet set.";
                 _setMaxProtoVersion(100);
+            } else {
+                qCDebug(VehicleLog) << "Leaving _maxProtoVersion at current value" << _maxProtoVersion;
             }
         }
 
@@ -2449,6 +2403,66 @@ void Vehicle::_sendNextQueuedMavCommand(void)
 }
 
 
+void Vehicle::_handleCommandAck(mavlink_message_t& message)
+{
+    bool showError = false;
+
+    mavlink_command_ack_t ack;
+    mavlink_msg_command_ack_decode(&message, &ack);
+
+    if (ack.command == MAV_CMD_REQUEST_AUTOPILOT_CAPABILITIES && ack.result != MAV_RESULT_ACCEPTED) {
+        // We aren't going to get a response back for capabilities, so stop waiting for it before we ask for mission items
+        qCDebug(VehicleLog) << QStringLiteral("Vehicle responded to MAV_CMD_REQUEST_AUTOPILOT_CAPABILITIES with error(%1). Setting no capabilities. Starting Plan request.").arg(ack.result);
+        _setCapabilities(0);
+    }
+
+    if (ack.command == MAV_CMD_REQUEST_PROTOCOL_VERSION && ack.result != MAV_RESULT_ACCEPTED) {
+        // The autopilot does not understand the request and consequently is likely handling only
+        // MAVLink 1
+        qCDebug(VehicleLog) << QStringLiteral("Vehicle responded to MAV_CMD_REQUEST_PROTOCOL_VERSION with error(%1).").arg(ack.result);
+        if (_maxProtoVersion == 0) {
+            qCDebug(VehicleLog) << "Setting _maxProtoVersion to 100 since not yet set.";
+            _setMaxProtoVersion(100);
+        } else {
+            qCDebug(VehicleLog) << "Leaving _maxProtoVersion at current value" << _maxProtoVersion;
+        }
+        // FIXME: Is this missing here. I believe it is a bug. Debug to verify. May need to go into Stable.
+        //_startPlanRequest();
+    }
+
+    if (_mavCommandQueue.count() && ack.command == _mavCommandQueue[0].command) {
+        _mavCommandAckTimer.stop();
+        showError = _mavCommandQueue[0].showError;
+        _mavCommandQueue.removeFirst();
+    }
+
+    emit mavCommandResult(_id, message.compid, ack.command, ack.result, false /* noResponsefromVehicle */);
+
+    if (showError) {
+        QString commandName = _toolbox->missionCommandTree()->friendlyName((MAV_CMD)ack.command);
+
+        switch (ack.result) {
+        case MAV_RESULT_TEMPORARILY_REJECTED:
+            qgcApp()->showMessage(tr("%1 command temporarily rejected").arg(commandName));
+            break;
+        case MAV_RESULT_DENIED:
+            qgcApp()->showMessage(tr("%1 command denied").arg(commandName));
+            break;
+        case MAV_RESULT_UNSUPPORTED:
+            qgcApp()->showMessage(tr("%1 command not supported").arg(commandName));
+            break;
+        case MAV_RESULT_FAILED:
+            qgcApp()->showMessage(tr("%1 command failed").arg(commandName));
+            break;
+        default:
+            // Do nothing
+            break;
+        }
+    }
+
+    _sendNextQueuedMavCommand();
+}
+
 void Vehicle::setPrearmError(const QString& prearmError)
 {
     _prearmError = prearmError;
diff --git a/src/comm/MAVLinkProtocol.cc b/src/comm/MAVLinkProtocol.cc
index 6175a52ef97ae077b56a66100ab902cfd72696b3..da4fe7d7fb11559afee5efe7cbdffb42376ae243 100644
--- a/src/comm/MAVLinkProtocol.cc
+++ b/src/comm/MAVLinkProtocol.cc
@@ -382,8 +382,6 @@ void MAVLinkProtocol::_vehicleCountChanged(void)
     if (count == 0) {
         // Last vehicle is gone, close out logging
         _stopLogging();
-        // Reset protocol version handling
-        _current_version = 0;
         _radio_version_mismatch_count = 0;
     }
 }