I ran into the same issue. This patch fixed it for me.

diff --git a/Modules/makesetup b/Modules/makesetup
index eac97ad134..0fbac03833 100755
--- a/Modules/makesetup
+++ b/Modules/makesetup
@@ -133,6 +133,7 @@ sed -e 's/[         ]*#.*//' -e '/^[        ]*$/d' |
 
                # Output DEFS in reverse order so first definition overrides
                case $line in
+               *-D*) ;;
                *=*)    DEFS="$line$NL$DEFS"; continue;;
                'include '*)    DEFS="$line$NL$DEFS"; continue;;
                '*noobjects*')