diff --git a/IPython/config/application.py b/IPython/config/application.py
index 0917d16..ec9431c 100644
--- a/IPython/config/application.py
+++ b/IPython/config/application.py
@@ -355,8 +355,6 @@ def boolean_flag(name, configurable, set_help='', unset_help=''):
     
     cls,trait = configurable.split('.')
     
-    setter = Config()
-    setter[cls][trait] = True
-    unsetter = Config()
-    unsetter[cls][trait] = False
+    setter = {cls : {trait : True}}
+    unsetter = {cls : {trait : False}}
     return {name : (setter, set_help), 'no-'+name : (unsetter, unset_help)}
diff --git a/IPython/config/loader.py b/IPython/config/loader.py
index edf40ef..2a0238f 100644
--- a/IPython/config/loader.py
+++ b/IPython/config/loader.py
@@ -408,8 +408,10 @@ class KeyValueConfigLoader(CommandLineConfigLoader):
                 if cfg is None:
                     raise ArgumentError("Unrecognized flag: %r"%item)
                 elif isinstance(cfg, (dict, Config)):
-                    # update self.config with Config:
-                    self.config.update(cfg)
+                    # don't clobber whole config sections, update
+                    # each section from config:
+                    for sec,c in cfg.iteritems():
+                        self.config[sec].update(c)
                 else:
                     raise ValueError("Invalid flag: %r"%flag)
             else:
diff --git a/IPython/config/tests/test_application.py b/IPython/config/tests/test_application.py
index c132bd9..31221eb 100644
--- a/IPython/config/tests/test_application.py
+++ b/IPython/config/tests/test_application.py
@@ -42,6 +42,7 @@ class Foo(Configurable):
 
 class Bar(Configurable):
 
+    b = Int(0, config=True, help="The integer b.")
     enabled = Bool(True, config=True, help="Enable bar.")
 
 
@@ -94,7 +95,7 @@ class TestApplication(TestCase):
         self.assertEquals(app.foo.j, 10)
         self.assertEquals(app.bar.enabled, False)
 
-    def test_alias(self):
+    def test_flags(self):
         app = MyApp()
         app.parse_command_line(["--disable"])
         app.init_bar()
@@ -103,3 +104,26 @@ class TestApplication(TestCase):
         app.init_bar()
         self.assertEquals(app.bar.enabled, True)
     
+    def test_aliases(self):
+        app = MyApp()
+        app.parse_command_line(["i=5", "j=10"])
+        app.init_foo()
+        self.assertEquals(app.foo.i, 5)
+        app.init_foo()
+        self.assertEquals(app.foo.j, 10)
+    
+    def test_flag_clobber(self):
+        """test that setting flags doesn't clobber existing settings"""
+        app = MyApp()
+        app.parse_command_line(["Bar.b=5", "--disable"])
+        print app.config
+        app.init_bar()
+        self.assertEquals(app.bar.enabled, False)
+        self.assertEquals(app.bar.b, 5)
+        app.parse_command_line(["--enable", "Bar.b=10"])
+        print app.config
+        app.init_bar()
+        self.assertEquals(app.bar.enabled, True)
+        self.assertEquals(app.bar.b, 10)
+    
+
diff --git a/IPython/core/newapplication.py b/IPython/core/newapplication.py
index 8a897de..de61f70 100644
--- a/IPython/core/newapplication.py
+++ b/IPython/core/newapplication.py
@@ -233,13 +233,13 @@ base_aliases = dict(
 )
 
 base_flags = dict(
-    debug = ({'Application' : Config({'log_level' : logging.DEBUG})},
+    debug = ({'Application' : {'log_level' : logging.DEBUG}},
             "set log level to logging.DEBUG (maximize logging output)"),
-    quiet = ({'Application' : Config({'log_level' : logging.CRITICAL})},
+    quiet = ({'Application' : {'log_level' : logging.CRITICAL}},
             "set log level to logging.CRITICAL (minimize logging output)"),
-    init = ({'BaseIPythonApplication' : Config({
+    init = ({'BaseIPythonApplication' : {
                     'copy_config_files' : True,
-                    'auto_create' : True})
+                    'auto_create' : True}
             }, "Initialize profile with default config files")
 )