diff --git a/utils/python/CIME/SystemTests/system_tests_compare_two.py b/utils/python/CIME/SystemTests/system_tests_compare_two.py
index 2e5015d6980a..ef7019f63d2c 100644
--- a/utils/python/CIME/SystemTests/system_tests_compare_two.py
+++ b/utils/python/CIME/SystemTests/system_tests_compare_two.py
@@ -147,9 +147,11 @@ def build_phase(self, sharedlib_only=False, model_only=False):
         # builds.
         self._activate_case1()
         self.build_indv(sharedlib_only=sharedlib_only, model_only=model_only)
+
         # The following is needed when _case_two_setup has a case_setup call
         # despite sharing the build (e.g., to change NTHRDS)
         self._case2.set_value("BUILD_COMPLETE",True)
+        self._case2.flush()
 
     def run_phase(self):
         """