--- a/make/Init.gmk	Sat Oct 14 09:51:25 2017 +0100
+++ b/make/Init.gmk	Mon Oct 16 08:43:42 2017 +0200
@@ -267,8 +267,9 @@
 	  $(ECHO) "Re-running configure using default settings"
         endif
 	( cd $(OUTPUTDIR) && PATH="$(ORIGINAL_PATH)" \
+	    CUSTOM_ROOT="$(CUSTOM_ROOT)" \
 	    CUSTOM_CONFIG_DIR="$(CUSTOM_CONFIG_DIR)" \
-	    $(BASH) $(CONFIGURE_CMD) $(CONFIGURE_COMMAND_LINE) )
+	    $(BASH) $(TOPDIR)/configure $(CONFIGURE_COMMAND_LINE) )
 
   ##############################################################################
   # The main target, for delegating into Main.gmk