diff --git a/src/damaris/gui/DamarisGUI.py b/src/damaris/gui/DamarisGUI.py
index d867be4..d622ca8 100644
--- a/src/damaris/gui/DamarisGUI.py
+++ b/src/damaris/gui/DamarisGUI.py
@@ -471,9 +471,10 @@ class DamarisGUI:
 
         self.id = self.lockfile.add_experiment()
         while not self.lockfile.am_i_next():
-            self.stop_experiment_flag.wait(interval)
             while gtk.events_pending():
                 gtk.main_iteration_do(False)
+            if self.stop_experiment_flag.wait(interval):
+                break
             if loop_run > 1:
                 self.experiment_script_statusbar_label.set_text("Waiting for other experiment to finish")
                 loop_run = 0
@@ -524,7 +525,10 @@ class DamarisGUI:
                 print("waiting for threads stoping...", end=' ')
                 still_running = [x for x in [ self.si.exp_handling, self.si.res_handling, self.si.back_driver ] if x is not None and x.is_alive( )]
                 for t in still_running:
-                    t.join( )
+                    while t.is_alive():
+                        while gtk.events_pending():
+                            gtk.main_iteration_do(False)
+                        t.join( 0.05 )
                 print("done")
 
             # cleanup
@@ -3312,6 +3316,8 @@ class ScriptInterface:
                 self.back_driver.start( )
                 while (not self.back_driver.quit_flag.isSet( ) and \
                                    (self.back_driver.core_pid is None or self.back_driver.core_pid <= 0)):
+                    while gtk.events_pending():
+                        gtk.main_iteration_do(False)
                     self.back_driver.quit_flag.wait( 0.1 )
             if self.exp_handling:
                 self.exp_handling.start( )