diff --git a/GUI.NET/Forms/frmConfigWizard.cs b/GUI.NET/Forms/frmConfigWizard.cs
index c64f3320..863644ad 100644
--- a/GUI.NET/Forms/frmConfigWizard.cs
+++ b/GUI.NET/Forms/frmConfigWizard.cs
@@ -148,7 +148,7 @@ namespace Mesen.GUI.Forms
 
 		private void lblCancel_Click(object sender, EventArgs e)
 		{
-			Application.Exit();
+			Close();
 		}
 
 		private void radStoragePortable_CheckedChanged(object sender, EventArgs e)
diff --git a/GUI.NET/Forms/frmMain.Help.cs b/GUI.NET/Forms/frmMain.Help.cs
index c8b96daf..6b0b5c26 100644
--- a/GUI.NET/Forms/frmMain.Help.cs
+++ b/GUI.NET/Forms/frmMain.Help.cs
@@ -120,7 +120,7 @@ namespace Mesen.GUI.Forms
 							this.BeginInvoke((MethodInvoker)(() => {
 								using(frmUpdatePrompt frmUpdate = new frmUpdatePrompt(currentVersion, latestVersion, changeLog, fileHash, donateText)) {
 									if(frmUpdate.ShowDialog(null, this) == DialogResult.OK) {
-										Application.Exit();
+										Close();
 									}
 								}
 							}));
diff --git a/GUI.NET/Program.cs b/GUI.NET/Program.cs
index b8be9e25..e20eb7a1 100644
--- a/GUI.NET/Program.cs
+++ b/GUI.NET/Program.cs
@@ -95,7 +95,6 @@ namespace Mesen.GUI
 					Application.Run(new frmConfigWizard());
 
 					if(ConfigManager.GetConfigFile() == null) {
-						Application.Exit();
 						return;
 					}
 				}
diff --git a/UpdateHelper/Program.cs b/UpdateHelper/Program.cs
index 609ed9d2..b845ebd3 100644
--- a/UpdateHelper/Program.cs
+++ b/UpdateHelper/Program.cs
@@ -19,6 +19,18 @@ namespace MesenUpdater
 				string backupDestFile = args[2];
 				bool isAdmin = args.Length > 3 && args[3] == "admin";
 
+				//Wait a bit for the application to shut down before trying to kill it
+				System.Threading.Thread.Sleep(1000);
+				try {
+					foreach(Process process in Process.GetProcessesByName("Mesen-S")) {
+						try {
+							if(process.MainModule.FileName == destFile) {
+								process.Kill();
+							}
+						} catch { }
+					}
+				} catch { }
+
 				int retryCount = 0;
 				while(retryCount < 10) {
 					try {