diff --git a/Code/Mantid/scripts/Inelastic/Direct/ISISDirecInelasticConfig.py b/Code/Mantid/scripts/Inelastic/Direct/ISISDirecInelasticConfig.py
index 9bffe08d63d2..2ac4f3b5b7db 100644
--- a/Code/Mantid/scripts/Inelastic/Direct/ISISDirecInelasticConfig.py
+++ b/Code/Mantid/scripts/Inelastic/Direct/ISISDirecInelasticConfig.py
@@ -4,6 +4,7 @@
 import re
 import copy
 from datetime import date
+import time
 
 # the list of instruments this configuration is applicable to
 INELASTIC_INSTRUMENTS = ['MAPS','LET','MERLIN','MARI','HET']
@@ -207,34 +208,26 @@ def config_need_replacing(self,config_file_name):
 #
     def script_need_replacing(self,source_script_name,target_script_name):
         """Method specifies conditions when existing reduction file should be replaced
-           by sample file
+           by a sample file.
         """
         if self._force_change_script:
             return True
-        # missing file should always be replaced
+        # non-existing file should always be replaced
         if not os.path.isfile(target_script_name):
            return True
-        # if user already started -- do not replace his config
-        #except when changes are forced
-        now_is =  date.today()
+        #Always replace sample file if it has not been touched
         start_date = self._user.get_start_date()
-        if now_is >start_date:
-            return False
-        #
-        time_targ = os.path.getmtime(target_script_name)
-
-        time_source = os.path.getmtime(source_script_name)
-        # we may want better granularity in a future
-#       source_mod_date = date.fromtimestamp(time_source)
-#       targ_mod_date = date.fromtimestamp(time_targ)
-        if time_targ < time_source:
+        # this time is set up to the file, copied from the repository
+        sample_file_time = time.mktime(start_date.timetuple())
+        targ_file_time  = os.path.getmtime(target_script_name)
+        if sample_file_time  ==  targ_file_time:
             return True
-        else:
+        else: # somebody have modified the target file. Leave it alone
             return False
 #
     def copy_reduction_sample(self,InstrName,CycleID,rb_folder):
-        """ Method copies sample reduction script from user script repository
-            to user folder.
+        """Method copies sample reduction script from user script repository
+           to user folder.
         """
 
         source_file = self._sample_reduction_file(InstrName)
@@ -254,8 +247,13 @@ def copy_reduction_sample(self,InstrName,CycleID,rb_folder):
             os.remove(full_target)
         shutil.copyfile(full_source,full_target)
         os.chmod(full_target,0777)
+
         if platform.system() != 'Windows':
             os.system('chown '+self._fedid+':'+self._fedid+' '+full_target)
+        # Set up the file  creation and modification dates to the users start date
+        start_date = self._user.get_start_date()
+        file_time = time.mktime(start_date.timetuple())
+        os.utime(full_target,(file_time,file_time))
 
 
     def get_data_folder_name(self,instr,cycle_ID):
diff --git a/Code/Mantid/scripts/test/ISISDirecInelasticConfigTest.py b/Code/Mantid/scripts/test/ISISDirecInelasticConfigTest.py
index b0bc01897dee..a05404a48040 100644
--- a/Code/Mantid/scripts/test/ISISDirecInelasticConfigTest.py
+++ b/Code/Mantid/scripts/test/ISISDirecInelasticConfigTest.py
@@ -227,7 +227,7 @@ def test_build_3Experiments_config(self):
             os.makedirs(user1RootDir)
         #
         user1 = UserProperties()
-        user1.set_user_properties('MARI','39990124','CYCLE39991',rbdir2)
+        user1.set_user_properties('MARI','20990124','CYCLE20991',rbdir2)
 
         mcf.init_user(user1ID,user1)
         source_file = self.makeFakeSourceReductionFile(mcf)
@@ -247,11 +247,14 @@ def test_build_3Experiments_config(self):
         target_file = mcf._target_reduction_file(instr,cycle_id)
         full_target_file = os.path.join(full_rb_path,target_file)
         self.assertTrue(os.path.exists(full_target_file))
-        # target file does not need replacing
+        # Fresh target file should always be replaced
+        self.assertTrue(mcf.script_need_replacing(source_file,full_target_file))
+        # modify target file access time:
+        access_time = os.path.getmtime(full_target_file)
+        now = time.time()
+        os.utime(full_target_file,(access_time ,now))
+        # should not replace modified target file
         self.assertFalse(mcf.script_need_replacing(source_file,full_target_file))
-        # make new fake configuration file
-        new_source = self.makeFakeSourceReductionFile(mcf,'New')
-        self.assertTrue(mcf.script_need_replacing(new_source,full_target_file))
 
         #--------------------------------------------------------------------
         # clean up