diff --git a/ArduCopter/GCS.h b/ArduCopter/GCS.h
index 0038d7dfea..5a37b3658f 100644
--- a/ArduCopter/GCS.h
+++ b/ArduCopter/GCS.h
@@ -122,6 +122,8 @@ public:
     // see if we should send a stream now. Called at 50Hz
     bool        stream_trigger(enum streams stream_num);
 
+    // call to reset the timeout window for entering the cli
+    void reset_cli_timeout();
 private:
     void        handleMessage(mavlink_message_t * msg);
 
@@ -192,6 +194,10 @@ private:
 
     // number of extra ticks to add to slow things down for the radio
     uint8_t         stream_slowdown;
+
+    // millis value to calculate cli timeout relative to.
+    // exists so we can separate the cli entry time from the system start time
+    uint32_t _cli_timeout;
 };
 
 #endif // __GCS_H
diff --git a/ArduCopter/GCS_Mavlink.pde b/ArduCopter/GCS_Mavlink.pde
index 4d0f82e9eb..7d98ebbda3 100644
--- a/ArduCopter/GCS_Mavlink.pde
+++ b/ArduCopter/GCS_Mavlink.pde
@@ -849,6 +849,7 @@ GCS_MAVLINK::init(AP_HAL::UARTDriver* port)
         chan = MAVLINK_COMM_1;
     }
     _queued_parameter = NULL;
+    reset_cli_timeout();
 }
 
 void
@@ -867,7 +868,7 @@ GCS_MAVLINK::update(void)
 #if CLI_ENABLED == ENABLED
         /* allow CLI to be started by hitting enter 3 times, if no
          *  heartbeat packets have been received */
-        if (mavlink_active == false) {
+        if (mavlink_active == 0 && (millis() - _cli_timeout) < 30000) {
             if (c == '\n' || c == '\r') {
                 crlf_count++;
             } else {
@@ -2178,6 +2179,10 @@ GCS_MAVLINK::queued_waypoint_send()
     }
 }
 
+void GCS_MAVLINK::reset_cli_timeout() {
+      _cli_timeout = millis();
+}
+
 /*
  *  a delay() callback that processes MAVLink packets. We set this as the
  *  callback in long running library initialisation routines to allow
diff --git a/ArduCopter/system.pde b/ArduCopter/system.pde
index 8c15056ae8..2b27e5cdf8 100644
--- a/ArduCopter/system.pde
+++ b/ArduCopter/system.pde
@@ -181,6 +181,7 @@ static void init_ardupilot()
     } else if (DataFlash.NeedErase()) {
         gcs_send_text_P(SEVERITY_LOW, PSTR("ERASING LOGS"));
         do_erase_logs();
+        gcs0.reset_cli_timeout();
     }
     if (g.log_bitmask != 0) {
         DataFlash.start_new_log();