diff --git a/jes/python/jes/core/interpreter/__init__.py b/jes/python/jes/core/interpreter/__init__.py
index a08fd09..b7fa6a9 100644
--- a/jes/python/jes/core/interpreter/__init__.py
+++ b/jes/python/jes/core/interpreter/__init__.py
@@ -172,6 +172,8 @@ def cleanup(self):
 
     def tryStop(self):
         self.stopSignal = True
+        from jes.gui.commandwindow.prompt import promptService
+        promptService.commandWindow.cancelPrompt()
         self.stop()
 
 
diff --git a/jes/python/jes/program.py b/jes/python/jes/program.py
index 2e7f019..dc70c5e 100644
--- a/jes/python/jes/program.py
+++ b/jes/python/jes/program.py
@@ -28,6 +28,7 @@
 from code import compile_command
 from tokenize import TokenError
 from java.lang import System
+from java.lang import Thread 
 from javax.swing import JOptionPane
 from jes.bridge.replbuffer import REPLBuffer
 from jes.bridge.terpactions import addInterpreterActions
@@ -143,7 +144,10 @@ def getVarsToHighlight(self):
 
     def initializeInterpreter(self, terp):
         startup = JESResources.getPathTo('python/jes/user-startup.py')
-        terp.runFile(startup, False)
+        #terp.runFile(startup, False)
+        #Henry Rachootin did this. This way, everything will be loaded before we start using it.
+        startupThread = terp.runFile(startup, False)
+        startupThread.join()
 
 ##########################################################################
 # Function name: loadFile