diff --git a/chrome/content/zotero/xpcom/dataDirectory.js b/chrome/content/zotero/xpcom/dataDirectory.js
index 8860663c9..5655fd279 100644
--- a/chrome/content/zotero/xpcom/dataDirectory.js
+++ b/chrome/content/zotero/xpcom/dataDirectory.js
@@ -576,7 +576,13 @@ Zotero.DataDirectory = {
 		// This can seemingly fail due to a race condition building the Standalone window,
 		// so just ignore it if it does
 		try {
-			Zotero.showZoteroPaneProgressMeter(Zotero.getString("dataDir.migration.inProgress"));
+			Zotero.showZoteroPaneProgressMeter(
+				Zotero.getString("dataDir.migration.inProgress"),
+				false,
+				null,
+				// Don't show message in a popup in Standalone if pane isn't ready
+				Zotero.iStandalone
+			);
 		}
 		catch (e) {
 			Zotero.logError(e);
diff --git a/chrome/content/zotero/xpcom/zotero.js b/chrome/content/zotero/xpcom/zotero.js
index a9ba161d6..41ad6cd75 100644
--- a/chrome/content/zotero/xpcom/zotero.js
+++ b/chrome/content/zotero/xpcom/zotero.js
@@ -1503,11 +1503,12 @@ Components.utils.import("resource://gre/modules/osfile.jsm");
 	/**
 	 * Show Zotero pane overlay and progress bar in all windows
 	 *
-	 * @param	{String}		msg
-	 * @param	{Boolean}		[determinate=false]
+	 * @param {String} msg
+	 * @param {Boolean} [determinate=false]
+	 * @param {Boolean} [modalOnly=false] - Don't use popup if Zotero pane isn't showing
 	 * @return	void
 	 */
-	this.showZoteroPaneProgressMeter = function (msg, determinate, icon) {
+	this.showZoteroPaneProgressMeter = function (msg, determinate, icon, modalOnly) {
 		// If msg is undefined, keep any existing message. If false/null/"", clear.
 		// The message is also cleared when the meters are hidden.
 		_progressMessage = msg = (msg === undefined ? _progressMessage : msg) || "";
@@ -1517,7 +1518,7 @@ Components.utils.import("resource://gre/modules/osfile.jsm");
 		while (enumerator.hasMoreElements()) {
 			var win = enumerator.getNext();
 			if(!win.ZoteroPane) continue;
-			if(!win.ZoteroPane.isShowing()) {
+			if (!win.ZoteroPane.isShowing() && !modalOnly) {
 				if (win != currentWindow) {
 					continue;
 				}