diff --git a/src/infrastructure/env/PhabricatorEnv.php b/src/infrastructure/env/PhabricatorEnv.php
--- a/src/infrastructure/env/PhabricatorEnv.php
+++ b/src/infrastructure/env/PhabricatorEnv.php
@@ -202,6 +202,12 @@
       phutil_load_library($library);
     }
 
+    // Drop any class map caches, since they will have generated without
+    // any classes from libraries. Without this, preflight setup checks can
+    // cause generation of a setup check cache that omits checks defined in
+    // libraries, for example.
+    PhutilClassMapQuery::deleteCaches();
+
     // If custom libraries specify config options, they won't get default
     // values as the Default source has already been loaded, so we get it to
     // pull in all options from non-phabricator libraries now they are loaded.