diff --git a/pyomo/common/config.py b/pyomo/common/config.py
index b01236bafaf..f8e43135a8e 100644
--- a/pyomo/common/config.py
+++ b/pyomo/common/config.py
@@ -1600,7 +1600,12 @@ def __call__(
 
         # ... and set the value, if appropriate
         if value is not NOTSET:
+            # Note that because we are *creating* a new Config object,
+            # we do not want set_value() to change the current (default)
+            # userSet flag for this object/container (see #3721).
+            tmp = ans._userSet
             ans.set_value(value)
+            ans._userSet = tmp
         return ans
 
     def name(self, fully_qualified=False):
diff --git a/pyomo/common/tests/test_config.py b/pyomo/common/tests/test_config.py
index b1c4d341b2d..193f8ab340d 100644
--- a/pyomo/common/tests/test_config.py
+++ b/pyomo/common/tests/test_config.py
@@ -1599,6 +1599,24 @@ def test_UserValues_declare_subBlock(self):
         test = '\n'.join(x.name(True) for x in self.config.user_values())
         self.assertEqual(test, "")
 
+    def test_userValues_call_nonempty(self):
+        # See bug report in Pyomo/pyomo#3721
+        default = ConfigDict()
+        default.declare("filename", ConfigValue(default=None, domain=str))
+        cfg = default(value={"filename": "example.txt"})
+        names = [x.name(True) for x in cfg.user_values()]
+        self.assertEqual(names, ["filename"])
+        self.assertTrue(all(x is not cfg for x in cfg.user_values()))
+
+    def test_userValues_call_empty_then_set(self):
+        # See bug report in Pyomo/pyomo#3721
+        default = ConfigDict()
+        default.declare("filename", ConfigValue(default=None, domain=str))
+        cfg = default({})
+        cfg["filename"] = "example.txt"
+        names = [x.name(True) for x in cfg.user_values()]
+        self.assertEqual(names, ["filename"])
+
     @unittest.skipIf(not yaml_available, "Test requires PyYAML")
     def test_parseDisplayAndValue_default(self):
         test = _display(self.config)