diff -u b/core/lib/Drupal/Core/Config/ConfigImporter.php b/core/lib/Drupal/Core/Config/ConfigImporter.php
--- b/core/lib/Drupal/Core/Config/ConfigImporter.php
+++ b/core/lib/Drupal/Core/Config/ConfigImporter.php
@@ -179,6 +179,7 @@
     $this->processedExtensions = $this->getEmptyExtensionsProcessedList();
     $this->createExtensionChangelist();
     $this->validated = FALSE;
+    $this->processedSystemTheme = FALSE;
     return $this;
   }
 
@@ -407,7 +408,7 @@
         throw new ConfigImporterException(sprintf('%s is already importing', static::LOCK_ID));
       }
 
-      // Where to put this?
+      // Process any extension changes before importing configuration.
       $this->handleExtensions();
 
       // First pass deleted, then new, and lastly changed configuration, in order
diff -u b/core/lib/Drupal/Core/Config/ConfigInstaller.php b/core/lib/Drupal/Core/Config/ConfigInstaller.php
--- b/core/lib/Drupal/Core/Config/ConfigInstaller.php
+++ b/core/lib/Drupal/Core/Config/ConfigInstaller.php
@@ -147,12 +147,10 @@
 
           // If we are syncing do not create configuration entities. Pluggable
           // configuration entities can have dependencies on modules that are
-          // not yet enabled. In the absence of dependency management for config
-          // entities this is a good as we can do. The problem with this
-          // approach is that any code that expects default configuration
-          // entities to exist (even if there is code the prevents this from
-          // happening) will be unstable after the module has been enabled and
-          // before the config entity has been imported.
+          // not yet enabled. This approach means that any code that expects
+          // default configuration entities to exist will be unstable after the
+          // module has been enabled and before the config entity has been
+          // imported.
           if ($this->isSyncing) {
             continue;
           }
diff -u b/core/lib/Drupal/Core/Config/StorageComparer.php b/core/lib/Drupal/Core/Config/StorageComparer.php
--- b/core/lib/Drupal/Core/Config/StorageComparer.php
+++ b/core/lib/Drupal/Core/Config/StorageComparer.php
@@ -6,6 +6,8 @@
  */
 
 namespace Drupal\Core\Config;
+
+use Drupal\Component\Utility\String;
 use Drupal\Core\Config\Entity\ConfigDependencyManager;
 
 /**
@@ -119,14 +121,21 @@
    * @param array $changes
    *   Array of changes to add to the changelist.
    * @param array $sort_order
-   *   Array to sort that can be used to sort the changelist.
+   *   Array to sort that can be used to sort the changelist. This array must
+   *   contain all the items that are in the change list.
    */
   protected function addChangeList($op, array $changes, array $sort_order = NULL) {
     // Only add changes that aren't already listed.
     $changes = array_diff($changes, $this->changelist[$op]);
     $this->changelist[$op] = array_merge($this->changelist[$op], $changes);
-    if (!empty($sort_order)) {
-      $this->changelist[$op] = array_intersect($sort_order, $this->changelist[$op]);
+    if (isset($sort_order)) {
+      $count = count($this->changelist[$op]);
+      // Sort the changlist in the same order as the $sort_order array and
+      // ensure the array is keyed from 0.
+      $this->changelist[$op] = array_values(array_intersect($sort_order, $this->changelist[$op]));
+      if ($count != count($this->changelist[$op])) {
+        throw \InvalidArgumentException(String::format('Sorting the @op changelist should not change its length.', array('@op' => $op)));
+      }
     }
   }
 
diff -u b/core/lib/Drupal/Core/Extension/ThemeHandler.php b/core/lib/Drupal/Core/Extension/ThemeHandler.php
--- b/core/lib/Drupal/Core/Extension/ThemeHandler.php
+++ b/core/lib/Drupal/Core/Extension/ThemeHandler.php
@@ -146,8 +146,12 @@
       // Refresh the theme list as installation of default configuration needs
       // an updated list to work.
       $this->reset();
-      // If we're not in a config synchronisation reset the source storage so
-      // that the extension install storage will pick up the new configuration.
+
+      // The default config installation storage only knows about the currently
+      // enabled list of themes, so it has to be reset in order to pick up the
+      // default config of the newly installed theme. However, do not reset the
+      // source storage when synchronizing configuration, since that would
+      // needlessly trigger a reload of the whole configuration to be imported.
       if (!$this->configInstaller->isSyncing()) {
         $this->configInstaller->resetSourceStorage();
       }
diff -u b/core/modules/config/tests/config_import_test/config_import_test.services.yml b/core/modules/config/tests/config_import_test/config_import_test.services.yml
--- b/core/modules/config/tests/config_import_test/config_import_test.services.yml
+++ b/core/modules/config/tests/config_import_test/config_import_test.services.yml
@@ -6 +6 @@
-    arguments: ['@state']
\ No newline at end of file
+    arguments: ['@state']