diff --git a/tools/configure.sh b/tools/configure.sh
index a91da260e4..2a98edbe69 100755
--- a/tools/configure.sh
+++ b/tools/configure.sh
@@ -205,7 +205,11 @@ install -m 644 "${src_config}" "${dest_config}" || \
 # file
 
 if [ "X${defappdir}" = "Xy" ]; then
-  sed -i -e "/^CONFIG_APPS_DIR/d" "${dest_config}"
+  # In-place edit can mess up permissions on Windows
+  # sed -i -e "/^CONFIG_APPS_DIR/d" "${dest_config}"
+  sed -e "/^CONFIG_APPS_DIR/d" "${dest_config}" > "${dest_config}-temp"
+  mv "${dest_config}-temp" "${dest_config}"
+
   echo "" >> "${dest_config}"
   echo "# Application configuration" >> "${dest_config}"
   echo "" >> "${dest_config}"