diff --git a/CIME/test_scheduler.py b/CIME/test_scheduler.py
index 2f05d946e03..acad9b9aba0 100644
--- a/CIME/test_scheduler.py
+++ b/CIME/test_scheduler.py
@@ -166,6 +166,20 @@ def _order_tests_by_runtime(tests, baseline_root):
     )
 
 
+###############################################################################
+def _run_cmpgen_namelists(test_dir):
+    ###############################################################################
+    env = os.environ.copy()
+    env["PYTHONPATH"] = f"{get_cime_root()}:{get_tools_path()}"
+    cmdstat, output, _ = run_cmd(
+        "./case.cmpgen_namelists",
+        combine_output=True,
+        from_dir=test_dir,
+        env=env,
+    )
+    return cmdstat, output
+
+
 ###############################################################################
 class TestScheduler(object):
     ###############################################################################
@@ -998,24 +1012,11 @@ def _setup_phase(self, test):
             test, "./case.setup", SETUP_PHASE, from_dir=test_dir
         )
 
-        # It's OK for this command to fail with baseline diffs but not catastrophically
+        # cmpgen_namelists is called again with checks later in _setup_phase(). This call is
+        # necessary for the correct behavior of --skip-tests-with-existing-baselines, and we don't
+        # need to check it for errors.
         if rv[0]:
-            env = os.environ.copy()
-            env["PYTHONPATH"] = f"{get_cime_root()}:{get_tools_path()}"
-            cmdstat, output, _ = run_cmd(
-                "./case.cmpgen_namelists",
-                combine_output=True,
-                from_dir=test_dir,
-                env=env,
-            )
-            try:
-                expect(
-                    cmdstat in [0, TESTS_FAILED_ERR_CODE],
-                    "Fatal error in case.cmpgen_namelists: {}".format(output),
-                )
-            except Exception:
-                self._update_test_status_file(test, SETUP_PHASE, TEST_FAIL_STATUS)
-                raise
+            _run_cmpgen_namelists(test_dir)
 
         if self._single_exe:
             with Case(self._get_test_dir(test), read_only=False) as case:
@@ -1046,13 +1047,28 @@ def _sharedlib_build_phase(self, test):
                 )
 
         test_dir = self._get_test_dir(test)
-        return self._shell_cmd_for_phase(
+        result = self._shell_cmd_for_phase(
             test,
             "./case.build --sharedlib-only",
             SHAREDLIB_BUILD_PHASE,
             from_dir=test_dir,
         )
 
+        # It's OK for this command to fail with baseline diffs but not catastrophically
+        env = os.environ.copy()
+        env["PYTHONPATH"] = f"{get_cime_root()}:{get_tools_path()}"
+        cmdstat, output = _run_cmpgen_namelists(test_dir)
+        try:
+            expect(
+                cmdstat in [0, TESTS_FAILED_ERR_CODE],
+                "Fatal error in case.cmpgen_namelists: {}".format(output),
+            )
+        except Exception:
+            self._update_test_status_file(test, SETUP_PHASE, TEST_FAIL_STATUS)
+            raise
+
+        return result
+
     ###########################################################################
     def _get_build_group(self, test):
         ###########################################################################