diff --git a/extras/Projucer/Source/ProjectSaving/jucer_ProjectSaver.h b/extras/Projucer/Source/ProjectSaving/jucer_ProjectSaver.h
index 6850deb6e6..81a54fcdc6 100644
--- a/extras/Projucer/Source/ProjectSaving/jucer_ProjectSaver.h
+++ b/extras/Projucer/Source/ProjectSaving/jucer_ProjectSaver.h
@@ -89,7 +89,6 @@ public:
         if (errors.size() == 0)
         {
             writeMainProjectFile();
-            project.updateModificationTime();
 
             writeAppConfigFile (modules, appConfigUserContent);
             writeBinaryDataFiles();
@@ -98,6 +97,9 @@ public:
             writeProjects (modules, specifiedExporterToSave, ! showProgressBox);
             writeAppConfigFile (modules, appConfigUserContent); // (this is repeated in case the projects added anything to it)
 
+            writeMainProjectFile(); // this is repeated so that the config flags are written correctly
+            project.updateModificationTime();
+
             if (generatedCodeFolder.exists())
                 writeReadmeFile();
         }