diff --git a/app/js/app-menu.js b/app/js/app-menu.js
index 35e4ffae..115c7f42 100644
--- a/app/js/app-menu.js
+++ b/app/js/app-menu.js
@@ -1486,16 +1486,14 @@ module.exports = function() {
       var chiseInstance = appUtilities.getActiveChiseInstance();
 
       // if there is no element in the cy instance, then return directly
+      var cy = chiseInstance.getCy();
       if(cy.elements().length == 0) {
         return;
       }
       console.log("layout-spinner")
       chiseInstance.startSpinner("layout-spinner")
 
-      // use the associated cy instance
       setTimeout(() => {
-      var cy = chiseInstance.getCy();
-
       // get current general properties for cy
       var currentGeneralProperties = appUtilities.getScratch(cy, 'currentGeneralProperties');
       var preferences = {
@@ -1510,22 +1508,16 @@ module.exports = function() {
       // use active chise instance
       var chiseInstance = appUtilities.getActiveChiseInstance();
 
-      // TODO think whether here is the right place to start the spinner
-      chiseInstance.startSpinner("layout-spinner");
-
-      // use the associated cy instance
-      setTimeout(() => {
-      var cy = chiseInstance.getCy();
-
       // if there is no element in the cy instance, then return directly
+      var cy = chiseInstance.getCy();
       if(cy.elements().length == 0) {
         return;
       }
+      chiseInstance.startSpinner("layout-spinner");
+
+      setTimeout(() => {
       // get current general properties for cy
       var currentGeneralProperties = appUtilities.getScratch(cy, 'currentGeneralProperties');      
-
-      
-
       var preferences = {
         quality: (cy.nodes().length > 3000 || cy.edges().length > 3000) ? "draft" : "default",
         animate: (cy.nodes().length > 3000 || cy.edges().length > 3000) ? false : currentGeneralProperties.animateOnDrawingChanges,
diff --git a/app/js/backbone-views.js b/app/js/backbone-views.js
index 3359425c..4b0e9d3c 100644
--- a/app/js/backbone-views.js
+++ b/app/js/backbone-views.js
@@ -4354,8 +4354,13 @@ var PromptConfirmationView = Backbone.View.extend({
     $(document)
       .off("click", "#prompt-confirmation-accept")
       .on("click", "#prompt-confirmation-accept", function (evt) {
-        afterFunction();
         $(self.el).modal("toggle");
+        
+        // This timeout is to insure that the modal disappers properly. 
+        // Without this sometimes there would be weird behavior on file loading.
+        setTimeout(() => {
+          afterFunction();
+        }, 500);
       });
 
     $(document)