diff --git a/IPython/core/inputsplitter.py b/IPython/core/inputsplitter.py
index eebbb7e..dc57840 100644
--- a/IPython/core/inputsplitter.py
+++ b/IPython/core/inputsplitter.py
@@ -545,9 +545,9 @@ class IPythonInputSplitter(InputSplitter):
     def transforms_in_use(self):
         """Transformers, excluding logical line transformers if we're in a
         Python line."""
-        t = self.physical_line_transforms + [self.assemble_logical_lines]
+        t = self.physical_line_transforms[:]
         if not self.within_python_line:
-            t += self.logical_line_transforms
+            t += [self.assemble_logical_lines] + self.logical_line_transforms
         return t + [self.assemble_python_lines] + self.python_line_transforms
 
     def reset(self):
@@ -556,6 +556,7 @@ class IPythonInputSplitter(InputSplitter):
         self._buffer_raw[:] = []
         self.source_raw = ''
         self.transformer_accumulating = False
+        self.within_python_line = False
         for t in self.transforms:
             t.reset()
     
@@ -685,11 +686,11 @@ class IPythonInputSplitter(InputSplitter):
             if line is None:
                 return _accumulating(transformer)
         
-        line = self.assemble_logical_lines.push(line)
-        if line is None:
-            return _accumulating('acc logical line')
-        
         if not self.within_python_line:
+            line = self.assemble_logical_lines.push(line)
+            if line is None:
+                return _accumulating('acc logical line')        
+        
             for transformer in self.logical_line_transforms:
                 line = transformer.push(line)
                 if line is None:
diff --git a/IPython/core/inputtransformer.py b/IPython/core/inputtransformer.py
index f5a9fe5..4606623 100644
--- a/IPython/core/inputtransformer.py
+++ b/IPython/core/inputtransformer.py
@@ -180,13 +180,15 @@ def assemble_logical_lines():
         
         parts = []
         while line is not None:
-            parts.append(line.rstrip('\\'))
-            if not line.endswith('\\'):
+            if line.endswith('\\') and (not has_comment(line)):
+                parts.append(line[:-1])
+                line = (yield None) # Get another line
+            else:
+                parts.append(line)
                 break
-            line = (yield None)
         
         # Output
-        line = ' '.join(parts)
+        line = ''.join(parts)
 
 # Utilities
 def _make_help_call(target, esc, lspace, next_input=None):
diff --git a/IPython/core/tests/test_inputtransformer.py b/IPython/core/tests/test_inputtransformer.py
index 48f15bf..2fddf97 100644
--- a/IPython/core/tests/test_inputtransformer.py
+++ b/IPython/core/tests/test_inputtransformer.py
@@ -190,11 +190,18 @@ syntax_ml = \
           ],
          ],
 
-       multiline_datastructure =
+       multiline_datastructure_prompt =
        [ [('>>> a = [1,','a = [1,'),
           ('... 2]','2]'),
          ],
        ],
+        
+       multiline_datastructure =
+       [ [('b = ("%s"', None),
+          ('# comment', None),
+          ('%foo )', 'b = ("%s"\n# comment\n%foo )'),
+         ],
+       ],
        
        leading_indent =
        [ [('    print "hi"','print "hi"'),
@@ -222,31 +229,31 @@ syntax_ml = \
        
        escaped =
        [ [('%abc def \\', None),
-          ('ghi', u_fmt("get_ipython().magic({u}'abc def  ghi')")),
+          ('ghi', u_fmt("get_ipython().magic({u}'abc def ghi')")),
           ],
          [('%abc def \\', None),
           ('ghi\\', None),
-          (None, u_fmt("get_ipython().magic({u}'abc def  ghi')")),
+          (None, u_fmt("get_ipython().magic({u}'abc def ghi')")),
           ],
        ],
        
        assign_magic =
        [ [(u'a = %bc de \\', None),
-          (u'fg', u_fmt("a = get_ipython().magic({u}'bc de  fg')")),
+          (u'fg', u_fmt("a = get_ipython().magic({u}'bc de fg')")),
           ],
          [(u'a = %bc de \\', None),
           (u'fg\\', None),
-          (None, u_fmt("a = get_ipython().magic({u}'bc de  fg')")),
+          (None, u_fmt("a = get_ipython().magic({u}'bc de fg')")),
           ],
        ],
        
        assign_system =
        [ [(u'a = !bc de \\', None),
-          (u'fg', u_fmt("a = get_ipython().getoutput({u}'bc de  fg')")),
+          (u'fg', u_fmt("a = get_ipython().getoutput({u}'bc de fg')")),
           ],
          [(u'a = !bc de \\', None),
           (u'fg\\', None),
-          (None, u_fmt("a = get_ipython().getoutput({u}'bc de  fg')")),
+          (None, u_fmt("a = get_ipython().getoutput({u}'bc de fg')")),
           ],
        ],
        )
@@ -262,7 +269,7 @@ def test_classic_prompt():
     tt.check_pairs(transform_and_reset(ipt.classic_prompt), syntax['classic_prompt'])
     for example in syntax_ml['classic_prompt']:
         transform_checker(example, ipt.classic_prompt)
-    for example in syntax_ml['multiline_datastructure']:
+    for example in syntax_ml['multiline_datastructure_prompt']:
         transform_checker(example, ipt.classic_prompt)
 
 
@@ -274,11 +281,13 @@ def test_ipy_prompt():
 def test_assemble_logical_lines():
     tests = \
     [ [(u"a = \\", None),
-       (u"123", u"a =  123"),
+       (u"123", u"a = 123"),
       ],
       [(u"a = \\", None),  # Test resetting when within a multi-line string
        (u"12 *\\", None),
-       (None, u"a =  12 *"),
+       (None, u"a = 12 *"),
+      ],
+      [(u"# foo\\", u"# foo\\"), # Comments can't be continued like this
       ],
     ]
     for example in tests:
@@ -300,7 +309,7 @@ def test_assemble_python_lines():
        (u"2,", None),
        (None, u"a = [1,\n2,"),
       ],
-    ]
+    ] + syntax_ml['multiline_datastructure']
     for example in tests:
         transform_checker(example, ipt.assemble_python_lines)