diff --git a/client/src/components/Masthead/initMasthead.js b/client/src/components/Masthead/initMasthead.js
index f4303bf5b7c..6b96f5d82cf 100644
--- a/client/src/components/Masthead/initMasthead.js
+++ b/client/src/components/Masthead/initMasthead.js
@@ -2,7 +2,7 @@
  * Temporary function used to mount the masthead inside the current application.
  * This function is exposed with the rest of the page-globals in bundledEntries.
  */
-import { mountMasthead } from "../../layout/masthead";
+import { mountMasthead } from "layout/masthead";
 import $ from "jquery";
 
 export function initMasthead(config, container) {
diff --git a/client/src/components/plugins/legacyNavigation.js b/client/src/components/plugins/legacyNavigation.js
index 3b31a75514f..ec514d74494 100644
--- a/client/src/components/plugins/legacyNavigation.js
+++ b/client/src/components/plugins/legacyNavigation.js
@@ -13,7 +13,7 @@ export function iframeAdd({ path, title = "Galaxy", $router = null }) {
     if (Galaxy.frame && Galaxy.frame.active) {
         Galaxy.frame.add({
             title: _l(title),
-            url: prependPath(path),
+            url: path,
         });
         return true;
     } else if ($router) {
diff --git a/client/src/layout/masthead.js b/client/src/layout/masthead.js
index 584de733725..45f0de3c29b 100644
--- a/client/src/layout/masthead.js
+++ b/client/src/layout/masthead.js
@@ -1,18 +1,23 @@
 import Masthead from "../components/Masthead/Masthead";
 import { mountVueComponent } from "../utils/mountVueComponent";
 import { fetchMenu } from "entry/analysis/menu";
-import { safePath } from "utils/redirect";
+import { WindowManager } from "layout/window-manager";
+import { getGalaxyInstance } from "app";
 
 export function mountMasthead(el, options) {
+    const windowManager = new WindowManager(options);
+    const Galaxy = getGalaxyInstance();
+    Galaxy.frame = windowManager;
     return mountVueComponent(Masthead)(
         {
             el: el,
             displayGalaxyBrand: options.display_galaxy_brand,
             baseTabs: fetchMenu(options),
             brand: options.brand,
-            brandLink: safePath(options.logo_url),
-            brandImage: safePath(options.logo_src),
-            brandImageSecondary: safePath(options.logo_src_secondary),
+            brandLink: options.logo_url,
+            brandImage: options.logo_src,
+            brandImageSecondary: options.logo_src_secondary,
+            windowTab: windowManager.getTab(),
         },
         el
     );
diff --git a/client/src/layout/window-manager.js b/client/src/layout/window-manager.js
index 3f63950dcc6..0ee2e49b40c 100644
--- a/client/src/layout/window-manager.js
+++ b/client/src/layout/window-manager.js
@@ -2,6 +2,7 @@
 import _l from "utils/localization";
 import WinBox from "winbox/src/js/winbox.js";
 import "winbox/dist/css/winbox.min.css";
+import { safePath } from "utils/redirect";
 
 export class WindowManager {
     constructor(options) {
@@ -25,27 +26,28 @@ export class WindowManager {
 
     /** Add and display a new window based on options. */
     add(options) {
+        const url = safePath(options.url);
         if (options.target == "_blank") {
-            window.open(options.url);
+            window.open(url);
         } else if (options.target == "_top" || options.target == "_parent" || options.target == "_self") {
-            window.location = options.url;
+            window.location = url;
         } else if (!this.active) {
             const $galaxy_main = window.parent.document.getElementById("galaxy_main");
             if (options.target == "galaxy_main" || options.target == "center") {
                 if ($galaxy_main.length === 0) {
-                    window.location = this._build_url(options.url, { use_panels: true });
+                    window.location = this._build_url(url, { use_panels: true });
                 } else {
-                    $galaxy_main.attr("src", options.url);
+                    $galaxy_main.attr("src", url);
                 }
             } else {
-                window.location = options.url;
+                window.location = url;
             }
         } else {
             this.counter++;
-            const url = this._build_url(options.url, { hide_panels: true, hide_masthead: true });
+            const boxUrl = this._build_url(url, { hide_panels: true, hide_masthead: true });
             WinBox.new({
                 title: options.title || "Window",
-                url: url,
+                url: boxUrl,
                 onclose: () => {
                     this.counter--;
                 },