diff --git a/src/main/java/unimelb/mf/client/sync/cli/MFInstrumentUpload.java b/src/main/java/unimelb/mf/client/sync/cli/MFInstrumentUpload.java
index 10e91610683ebe01177d6d2395777961a9c046e6..c12b9f1916f69d7238c8e1ceacb1cbf3e6d21aa0 100644
--- a/src/main/java/unimelb/mf/client/sync/cli/MFInstrumentUpload.java
+++ b/src/main/java/unimelb/mf/client/sync/cli/MFInstrumentUpload.java
@@ -123,6 +123,9 @@ public class MFInstrumentUpload extends MFSyncApp {
          * parse MF config
          */
         MFConfigurationBuilder mfConfig = new MFConfigurationBuilder();
+        if (mfConfig.app() == null) {
+            mfConfig.setApp(applicationName());
+        }
         mfConfig.loadFromXmlFile(configPath.toFile());
 
         /*
diff --git a/src/main/scripts/windows/unimelb-mf-instrument-upload.cmd b/src/main/scripts/windows/unimelb-mf-instrument-upload.cmd
index 3e62159319f3e9730e2050a8b3863a7e60479783..478a7b99031b860ede6c2b19382989dec2a565d1 100644
--- a/src/main/scripts/windows/unimelb-mf-instrument-upload.cmd
+++ b/src/main/scripts/windows/unimelb-mf-instrument-upload.cmd
@@ -9,4 +9,4 @@ popd
 
 set JAR=%ROOT%\lib\unimelb-mf-clients.jar
 
-java -Xmx1024m -cp "%JAR%" unimelb.mf.client.sync.cli.unimelb-mf-upload.cmd %*
+java -Xmx1024m -cp "%JAR%" unimelb.mf.client.sync.cli.MFInstrumentUpload %*