diff --git a/ROMFS/px4fmu_common/init.d/rcS b/ROMFS/px4fmu_common/init.d/rcS
index 9c66bb9202..16733fc000 100644
--- a/ROMFS/px4fmu_common/init.d/rcS
+++ b/ROMFS/px4fmu_common/init.d/rcS
@@ -498,6 +498,8 @@ unset PWM_MIN
 unset SDCARD_MIXERS_PATH
 unset USE_IO
 unset VEHICLE_TYPE
+unset BOARD_RC
+unset AUTOCNF
 
 #
 # Boot is complete, inform MAVLink app(s) that the system is now fully up and running.
diff --git a/Tools/serial/rc.serial.jinja b/Tools/serial/rc.serial.jinja
index 6a822c4ddc..6f3b9de05b 100644
--- a/Tools/serial/rc.serial.jinja
+++ b/Tools/serial/rc.serial.jinja
@@ -22,9 +22,13 @@ fi
 
 {% endfor %}
 
+{% for serial_device in serial_devices -%}
+unset PRT_{{ serial_device.tag }}_
+{% endfor %}
 unset i
 unset SERIAL_DEV
 unset PRT
 unset PRT_F
 unset BAUD_PARAM
+unset MAV_ARGS