diff --git a/IPython/iplib.py b/IPython/iplib.py
index ef2f044..b9d758e 100644
--- a/IPython/iplib.py
+++ b/IPython/iplib.py
@@ -1487,7 +1487,7 @@ class InteractiveShell(object,Magic):
             return True
         return ask_yes_no(prompt,default)
 
-    def cache_main_mod(self,mod):
+    def cache_main_mod(self,mod,fname=None):
         """Cache a main module.
 
         When scripts are executed via %run, we must keep a reference to their
@@ -1515,7 +1515,10 @@ class InteractiveShell(object,Magic):
         In [12]: IPython.__file__ in _ip.IP._user_main_modules
         Out[12]: True
         """
-        self._user_main_modules[os.path.abspath(mod.__file__) ] = mod
+        if fname is None:
+            fname = mod.__file__
+        #print >> sys.stderr, 'CFNAME  :', os.path.abspath(fname)  # dbg
+        self._user_main_modules[os.path.abspath(fname)] = mod
 
     def clear_main_mod_cache(self):
         """Clear the cache of main modules.
diff --git a/IPython/tests/test_magic.py b/IPython/tests/test_magic.py
index 4878710..cde72f4 100644
--- a/IPython/tests/test_magic.py
+++ b/IPython/tests/test_magic.py
@@ -131,3 +131,19 @@ def test_fail_dec2(*a,**k):
 def test_fail_dec3(*a,**k):
     yield nt.assert_true, False
 
+
+def doctest_refbug():
+    """Very nasty problem with references held by multiple runs of a script.
+    See: https://bugs.launchpad.net/ipython/+bug/269966
+
+    In [2]: run refbug
+
+    In [3]: call_f()
+    lowercased: hello
+
+    In [4]: run refbug
+
+    In [5]: call_f()
+    lowercased: hello
+    lowercased: hello
+    """