diff -u b/core/lib/Drupal/Core/Extension/ModuleHandler.php b/core/lib/Drupal/Core/Extension/ModuleHandler.php
--- b/core/lib/Drupal/Core/Extension/ModuleHandler.php
+++ b/core/lib/Drupal/Core/Extension/ModuleHandler.php
@@ -683,6 +683,12 @@
             ->setSyncing(TRUE)
             ->setSourceStorage($source_storage);
         }
+        else {
+          // If we're not in a config synchronisation reset the source storage
+          // so that the extension install storage will pick up the new
+          // configuration.
+          $config_installer->resetSourceStorage();
+        }
         \Drupal::service('config.installer')->installDefaultConfig('module', $module);
 
         // If the module has no current updates, but has some that were
only in patch2:
unchanged:
--- a/core/lib/Drupal/Core/Extension/ThemeHandler.php
+++ b/core/lib/Drupal/Core/Extension/ThemeHandler.php
@@ -145,6 +145,11 @@ public function enable(array $theme_list) {
       // Refresh the theme list as installation of default configuration needs
       // an updated list to work.
       $this->reset();
+      // If we're not in a config synchronisation reset the source storage so
+      // that the extension install storage will pick up the new configuration.
+      if (!$this->configInstaller->isSyncing()) {
+        $this->configInstaller->resetSourceStorage();
+      }
       // Install default configuration of the theme.
       $this->configInstaller->installDefaultConfig('theme', $key);
     }