diff --git a/quad/src/quad_app/control_algorithm.c b/quad/src/quad_app/control_algorithm.c
index 9f2c8d5b9fdca403877c8a11112024a1fc75db17..3a1ab4675a94b2703094e35e9be227508269a5ae 100644
--- a/quad/src/quad_app/control_algorithm.c
+++ b/quad/src/quad_app/control_algorithm.c
@@ -356,9 +356,9 @@ int control_algorithm_init(parameter_t * ps)
 	//memcpy(raw_actuator_struct->controller_corrected_motor_commands, user_input_struct->rc_commands, sizeof(int) * 6);
 
 	// don't use the PID corrections if the throttle is less than about 10% of its range
-
-    // re-enable the check for AUTO_FLIGHT_MODE when autonomous is fully enabled!!!
-	if((user_input_struct->rc_commands[THROTTLE] > 118000))
+    // unless we are in autonomous
+	if((user_input_struct->rc_commands[THROTTLE] > 118000) ||
+        user_defined_struct->flight_mode = AUTO_FLIGHT_MODE)
 	{
 			//THROTTLE
 
diff --git a/quad/src/quad_app/initialize_components.c b/quad/src/quad_app/initialize_components.c
index 967eaa6294b342641fc1dcdfb0b3327ea4490427..e476fd633eb9ecce40eb77af6570eac63462833a 100644
--- a/quad/src/quad_app/initialize_components.c
+++ b/quad/src/quad_app/initialize_components.c
@@ -21,14 +21,12 @@ int protection_loops(modular_structs_t *structs)
 	
 	struct PWMInputDriver *pwm_inputs = &structs->hardware_struct.pwm_inputs;
 	read_rec_all(pwm_inputs, rc_commands);
-
-	// wait for RC receiver to connect to transmitter
-	while(rc_commands[THROTTLE] < 75000)
-	  read_rec_all(pwm_inputs, rc_commands);
-
-	// wait until throttle is low and the gear switch is engaged (so you don't immediately break out of the main loop below)
-	// also wait for the flight mode to be set to manual
-	while(rc_commands[THROTTLE] > 125000 || read_kill(rc_commands[GEAR]) || !read_flap(rc_commands[FLAP])) {
+	
+	while(rc_commands[THROTTLE] < 75000 || // wait for RC receiver to connect to transmitter
+        rc_commands[THROTTLE] > 125000 || // Wait until throttle is low
+        read_kill(rc_commands[GEAR]) || // Wait until gear switch is engaged (so you don't immediately break out of the main loop below)
+        !read_flap(rc_commands[FLAP])) // Wait for the flight mode to be set to manual
+    {
 		process_received(structs);
 		read_rec_all(pwm_inputs, rc_commands);
 	}