diff --git a/mk/PX4/config_px4fmu-v2_APM.mk b/mk/PX4/config_px4fmu-v2_APM.mk
index 03e145418e..9a26e4c721 100644
--- a/mk/PX4/config_px4fmu-v2_APM.mk
+++ b/mk/PX4/config_px4fmu-v2_APM.mk
@@ -53,13 +53,16 @@ MODULES		+= systemcmds/tests
 MODULES		+= systemcmds/nshterm
 # the conditional allows for building with upstream master
 # which doesn't have auth
-ifneq ($(wildcard systemcmds/auth),)  
+ifneq ($(wildcard $(PX4_ROOT)/src/systemcmds/auth),)  
 MODULES		+= systemcmds/auth
 endif
 MODULES         += systemcmds/mtd
-ifneq ($(wildcard systemcmds/reflect),)  
+ifneq ($(wildcard $(PX4_ROOT)/src/systemcmds/reflect),)  
 MODULES         += systemcmds/reflect
 endif
+ifneq ($(wildcard $(PX4_ROOT)/src/systemcmds/motor_test),)  
+MODULES         += systemcmds/motor_test
+endif
 
 #
 # Library modules
@@ -70,7 +73,7 @@ MODULES		+= modules/uORB
 MODULES		+= lib/mathlib/math/filter
 # the conditional allows for building with upstream master
 # which doesn't have libtomcrypt and libtomfastmath
-ifneq ($(wildcard modules/libtomfastmath),)  
+ifneq ($(wildcard $(PX4_ROOT)/src/modules/libtomfastmath),)  
 MODULES	        += modules/libtomfastmath
 MODULES         += modules/libtomcrypt
 endif