--- a/ui/main.cpp	Thu Apr 24 10:39:09 2014 +0000
+++ b/ui/main.cpp	Thu Apr 24 12:45:11 2014 +0200
@@ -37,9 +37,25 @@
 {
     QApplication app (argc, argv);
 
+    QApplication::setQuitOnLastWindowClosed(false);
+    QApplication::setOrganizationName(QString::fromLatin1(ORGANIZATION));
+    QApplication::setApplicationName(QString::fromLatin1(APPNAME));
+    QApplication::setApplicationVersion(QString::fromLatin1(VERSION));
+    QSettings::setDefaultFormat(QSettings::IniFormat);
+
     QStringList arguments = QApplication::arguments();
     bool trayMode = arguments.contains("--tray");
 
+    QSettings settings;
+    settings.beginGroup("settings");
+    int autoStart = settings.value("autostart").toInt();
+    settings.endGroup();
+    qDebug() << "autostart: " << autoStart;
+
+    if (trayMode && autoStart <= 0) {
+        return 0;
+    }
+
     QTranslator translator;
     if (QLocale::system().name() == "C") {
         /* Useful for testing / development as the primary target is german */
@@ -60,12 +76,6 @@
         return 1;
     }
 
-    QApplication::setQuitOnLastWindowClosed(false);
-    QApplication::setOrganizationName(QString::fromLatin1(ORGANIZATION));
-    QApplication::setApplicationName(QString::fromLatin1(APPNAME));
-    QApplication::setApplicationVersion(QString::fromLatin1(VERSION));
-    QSettings::setDefaultFormat(QSettings::IniFormat);
-
     MainWindow mainWin(trayMode);
 
     return app.exec();

--- a/ui/mainwindow.cpp	Thu Apr 24 10:39:09 2014 +0000
+++ b/ui/mainwindow.cpp	Thu Apr 24 12:45:11 2014 +0200
@@ -347,7 +347,17 @@
     settingsLayout->addWidget(mAutoUpdateOption);
     settingsLayout->addWidget(mAutoStartOption);
     settingsBox->setLayout(settingsLayout);
-//    connect(autoUpdateOption, SIGNAL(stateChanged()), this, SLOT(setAutoUpdate()));
+    connect(mAutoUpdateOption, SIGNAL(stateChanged(int)),
+        this, SLOT(saveAutoUpdate(int)));
+    connect(mAutoStartOption, SIGNAL(stateChanged(int)),
+        this, SLOT(saveAutoStart(int)));
+    mSettings.beginGroup("settings");
+    int autoUpdate = mSettings.value("autoupdate").toInt();
+    int autoStart = mSettings.value("autostart").toInt();
+    mSettings.endGroup();
+    mAutoUpdateOption->setCheckState(autoUpdate > 0 ? Qt::Checked : Qt::Unchecked);
+    mAutoStartOption->setCheckState(autoStart > 0 ? Qt::Checked : Qt::Unchecked);
+
 
     // The buttons.
     bottomLayout->setAlignment(Qt::AlignBottom);
@@ -597,7 +607,10 @@
 
         mSettings.setValue("List/installed", listFileName);
         mSettings.setValue("List/installedDate", listFileDate);
+        mInstalledList = mListToInstall;
+        mListToInstall = CertificateList();
     }
+    loadCertificateList();
 }
 
 void MainWindow::installCerts() {
@@ -657,14 +670,18 @@
 
 bool MainWindow::saveUnselectedCertificates()
 {
+    mPreviouslyUnselected.clear();
     mSettings.beginGroup("unselected");
     mSettings.remove(""); /* Clears old choices */
     for (int i = 0; i < mCertListWidget->count(); i++) {
         QListWidgetItem *item = mCertListWidget->item(i);
         if (item->checkState() != Qt::Checked &&
             (item->flags() & Qt::ItemIsUserCheckable)) {
-            mSettings.setValue(QString::fromLatin1("cert%1").arg(i),
-                    item->data(CertificateItemDelegate::DataRole).value<Certificate>().base64Line());
+            QString key = QString::fromLatin1("cert%1").arg(i);
+            QString value =
+                item->data(CertificateItemDelegate::DataRole).value<Certificate>().base64Line();
+            mSettings.setValue(key, value);
+            mPreviouslyUnselected << value;
         }
     }
     mSettings.endGroup();
@@ -672,6 +689,20 @@
     return mSettings.status() == QSettings::NoError;
 }
 
+void MainWindow::saveAutoUpdate(int state)
+{
+    mSettings.beginGroup("settings");
+    mSettings.setValue("autoupdate", state);
+    mSettings.endGroup();
+}
+
+void MainWindow::saveAutoStart(int state)
+{
+    mSettings.beginGroup("settings");
+    mSettings.setValue("autostart", state);
+    mSettings.endGroup();
+}
+
 void MainWindow::closeApp()
 {
     saveUnselectedCertificates();

--- a/ui/mainwindow.h	Thu Apr 24 10:39:09 2014 +0000
+++ b/ui/mainwindow.h	Thu Apr 24 12:45:11 2014 +0200
@@ -80,6 +80,9 @@
     void installCerts();
     void newSWAvailable(const QString& fileName, const QDateTime& modDate);
 
+    void saveAutoUpdate(int state);
+    void saveAutoStart(int state);
+
     /** @brief saves the currently unselected certificates
      *
      * This creates / updates a qsettings section that