diff --git a/wlauto/tests/test_config.py b/wlauto/tests/test_config.py
index 0587ddb5..2c9f9ac3 100644
--- a/wlauto/tests/test_config.py
+++ b/wlauto/tests/test_config.py
@@ -167,6 +167,13 @@ class ConfigTest(TestCase):
         self.config.finalize()
         assert_equal(self.config.instrumentation['list_params']['param'], [0.1, 0.1, 0.1])
 
+    def test_remove_instrument(self):
+        self.config.load_config({'instrumentation': ['list_params']})
+        a = Agenda('{config: {instrumentation: [~list_params] }}')
+        self.config.set_agenda(a)
+        self.config.finalize()
+        assert_equal(self.config.instrumentation, {})
+
     def test_global_instrumentation(self):
         self.config.load_config({'instrumentation': ['global_instrument']})
         ws = AgendaWorkloadEntry(id='a', iterations=1, name='linpack', instrumentation=['local_instrument'])
diff --git a/wlauto/utils/misc.py b/wlauto/utils/misc.py
index 1eed15d8..6718fa78 100644
--- a/wlauto/utils/misc.py
+++ b/wlauto/utils/misc.py
@@ -339,6 +339,8 @@ def _merge_two_lists(base, other, duplicates='all', dict_type=dict):  # pylint:
     elif duplicates == 'first':
         base_norm = normalize(base, dict_type)
         merged_list = normalize(base, dict_type)
+        for v in base_norm:
+            _check_remove_item(merged_list, v)
         for v in normalize(other, dict_type):
             if not _check_remove_item(merged_list, v):
                 if v not in base_norm:
@@ -351,9 +353,12 @@ def _merge_two_lists(base, other, duplicates='all', dict_type=dict):  # pylint:
             if not _check_remove_item(merged_list, v):
                 if v not in other_norm:
                     merged_list.append(v)
-        return merged_list + other_norm
+        for v in other_norm:
+            if not _check_remove_item(merged_list, v):
+                merged_list.append(v)
+        return merged_list
     else:
-        raise ValueError('Unexpected value for list duplcates argument: {}. '.format(duplicates) +
+        raise ValueError('Unexpected value for list duplicates argument: {}. '.format(duplicates) +
                          'Must be in {"all", "first", "last"}.')