diff --git a/python/helpers/pydev/pydevd.py b/python/helpers/pydev/pydevd.py
index 6ab83b956790..d0919c18d9b6 100644
--- a/python/helpers/pydev/pydevd.py
+++ b/python/helpers/pydev/pydevd.py
@@ -1,6 +1,5 @@
 #IMPORTANT: pydevd_constants must be the 1st thing defined because it'll keep a reference to the original sys._getframe
 from __future__ import nested_scopes # Jython 2.1 support
-from pydevd_constants import * # @UnusedWildImport
 
 import pydev_monkey_qt
 from pydevd_utils import save_main_module
@@ -28,8 +27,7 @@ from pydevd_comm import  CMD_CHANGE_VARIABLE, \
                          CMD_STEP_INTO, \
                          CMD_STEP_OVER, \
                          CMD_STEP_RETURN, \
-                         CMD_THREAD_CREATE, \
-                         CMD_THREAD_KILL, \
+    CMD_THREAD_KILL, \
                          CMD_THREAD_RUN, \
                          CMD_THREAD_SUSPEND, \
                          CMD_RUN_TO_LINE, \
@@ -52,8 +50,7 @@ from pydevd_comm import  CMD_CHANGE_VARIABLE, \
                          InternalTerminateThread, \
                          InternalRunThread, \
                          InternalStepThread, \
-                         NetCommand, \
-                         NetCommandFactory, \
+    NetCommandFactory, \
                          PyDBDaemonThread, \
                          _queue, \
                          ReaderThread, \
@@ -65,8 +62,7 @@ from pydevd_comm import  CMD_CHANGE_VARIABLE, \
                          StartServer, \
                          InternalSetNextStatementThread, \
                          ReloadCodeCommand, \
-                         ID_TO_MEANING,\
-                         CMD_SET_PY_EXCEPTION, \
+    CMD_SET_PY_EXCEPTION, \
                          CMD_IGNORE_THROWN_EXCEPTION_AT,\
                          InternalGetBreakpointException, \
                          InternalSendCurrExceptionTrace,\
@@ -382,16 +378,16 @@ class PyDB:
 
     def haveAliveThreads(self):
         for t in threadingEnumerate():
-            if isinstance(t, PyDBDaemonThread):
-                pydev_log.error_once(
-                    'Error in debugger: Found PyDBDaemonThread through threading.enumerate().\n')
-                
             if getattr(t, 'is_pydev_daemon_thread', False):
                 #Important: Jython 2.5rc4 has a bug where a thread created with thread.start_new_thread won't be
                 #set as a daemon thread, so, we also have to check for the 'is_pydev_daemon_thread' flag.
                 #See: https://github.com/fabioz/PyDev.Debugger/issues/11
                 continue
-            
+
+            if isinstance(t, PyDBDaemonThread):
+                pydev_log.error_once(
+                    'Error in debugger: Found PyDBDaemonThread not marked with is_pydev_daemon_thread=True.\n')
+
             if isThreadAlive(t) and not t.isDaemon():
                 return True
 
@@ -495,7 +491,7 @@ class PyDB:
             _DebugConsoleHelper._return_control_osc = not _DebugConsoleHelper._return_control_osc
             return _DebugConsoleHelper._return_control_osc
 
-        from pydev_ipython.inputhook import get_inputhook, set_return_control_callback
+        from pydev_ipython.inputhook import set_return_control_callback
         set_return_control_callback(return_control)
 
         from pydev_import_hook import import_hook_manager
diff --git a/python/helpers/pydev/pydevd_comm.py b/python/helpers/pydev/pydevd_comm.py
index bf8e2db148df..b9db00e9fced 100644
--- a/python/helpers/pydev/pydevd_comm.py
+++ b/python/helpers/pydev/pydevd_comm.py
@@ -57,7 +57,6 @@ each command has a format:
     * JAVA - remote debugger, the java end
     * PYDB - pydevd, the python end
 '''
-import sys
 
 from pydevd_constants import * #@UnusedWildImport
 from _pydev_imps import _pydev_time as time, _pydev_thread
@@ -245,6 +244,8 @@ def SetGlobalDebugger(dbg):
 # PyDBDaemonThread
 #=======================================================================================================================
 class PyDBDaemonThread(threading.Thread):
+    created_pydb_daemon_threads = {}
+
     def __init__(self):
         threading.Thread.__init__(self)
         self.setDaemon(True)
@@ -253,13 +254,22 @@ class PyDBDaemonThread(threading.Thread):
         self.is_pydev_daemon_thread = True
 
     def run(self):
-        if sys.platform.startswith("java"):
-            import org.python.core as PyCore #@UnresolvedImport
-            ss = PyCore.PySystemState()
-            # Note: Py.setSystemState() affects only the current thread.
-            PyCore.Py.setSystemState(ss)
+        created_pydb_daemon = self.created_pydb_daemon_threads
+        created_pydb_daemon[self] = 1
+        try:
+            try:
+                if IS_JYTHON:
+                    import org.python.core as PyCore #@UnresolvedImport
+                    ss = PyCore.PySystemState()
+                    # Note: Py.setSystemState() affects only the current thread.
+                    PyCore.Py.setSystemState(ss)
 
-        self.OnRun()
+                self.OnRun()
+            except:
+                if sys is not None and traceback is not None:
+                    traceback.print_exc()
+        finally:
+            del created_pydb_daemon[self]
 
     def OnRun(self):
         raise NotImplementedError('Should be reimplemented by: %s' % self.__class__)
@@ -270,7 +280,18 @@ class PyDBDaemonThread(threading.Thread):
 
     def stopTrace(self):
         if self.dontTraceMe:
-            pydevd_tracing.SetTrace(None) # no debugging on this thread
+
+            disable_tracing = True
+
+            if pydevd_vm_type.GetVmType() == pydevd_vm_type.PydevdVmType.JYTHON and sys.hexversion <= 0x020201f0:
+                # don't run untraced threads if we're in jython 2.2.1 or lower
+                # jython bug: if we start a thread and another thread changes the tracing facility
+                # it affects other threads (it's not set only for the thread but globally)
+                # Bug: http://sourceforge.net/tracker/index.php?func=detail&aid=1870039&group_id=12867&atid=112867
+                disable_tracing = False
+
+            if disable_tracing:
+                pydevd_tracing.SetTrace(None)  # no debugging on this thread
 
 
 #=======================================================================================================================