diff --git a/flake8/options/manager.py b/flake8/options/manager.py
index f4bd1d8..6c0d036 100644
--- a/flake8/options/manager.py
+++ b/flake8/options/manager.py
@@ -149,12 +149,12 @@ class OptionManager(object):
     def parse_args(self, args=None, values=None):
         """Simple proxy to calling the OptionParser's parse_args method."""
         options, xargs = self.parser.parse_args(args, values)
-        for config_name, option in self.config_options_dict.items():
-            dest = option.dest or config_name
-            if self.normalize_paths:
+        for option in self.options:
+            dest = option.dest
+            if option.normalize_paths:
                 old_value = getattr(options, dest)
                 setattr(options, dest, utils.normalize_paths(old_value))
-            elif self.comma_separated_list:
+            elif option.comma_separated_list:
                 old_value = getattr(options, dest)
                 setattr(options, dest,
                         utils.parse_comma_separated_list(old_value))
diff --git a/tests/unit/test_option_manager.py b/tests/unit/test_option_manager.py
index 4983c1d..37c9570 100644
--- a/tests/unit/test_option_manager.py
+++ b/tests/unit/test_option_manager.py
@@ -1,5 +1,6 @@
 """Unit tests for flake.options.manager.OptionManager."""
 import optparse
+import os
 
 import pytest
 
@@ -57,3 +58,19 @@ def test_add_option_with_custom_args(optmanager):
     attrs = ['parse_from_config', 'comma_separated_list', 'normalize_paths']
     for option, attr in zip(optmanager.options, attrs):
         assert getattr(option, attr) is True
+
+
+def test_parse_args(optmanager):
+    assert optmanager.options == []
+    assert optmanager.config_options_dict == {}
+
+    optmanager.add_option('-v', '--verbose', action='count')
+    optmanager.add_option('--config', normalize_paths=True)
+    optmanager.add_option('--exclude', default='E123,W234',
+                          comma_separated_list=True)
+
+    options, args = optmanager.parse_args(
+        ['-v', '-v', '-v', '--config', '../config.ini']
+    )
+    assert options.verbose == 3
+    assert options.config == os.path.abspath('../config.ini')