diff --git a/includes/common.inc b/includes/common.inc
index 9346e6a..5087617 100644
--- a/includes/common.inc
+++ b/includes/common.inc
@@ -5255,11 +5255,22 @@ function _drupal_bootstrap_full() {
     // - The theme can have hook_*_alter() implementations affect page building
     //   (e.g., hook_form_alter(), hook_node_view_alter(), hook_page_alter()),
     //   ahead of when rendering starts.
-    menu_set_custom_theme();
+    $custom_theme = menu_set_custom_theme();
+    // If the custom theme is set and the base theme is set and they differ,
+    // reset the theme.
+    global $theme;
+    if (!empty($custom_theme) && !empty($theme) && $custom_theme != $theme) {
+      drupal_static_reset('theme_get_registry');
+      $drupal_static_fast['registry'] = &drupal_static('theme_get_registry');
+      $drupal_static_fast['registry'] = array();
+      drupal_static_reset('drupal_add_js');
+      drupal_static_reset('drupal_add_css');
+      unset($GLOBALS['theme']);
+    }
     // Initialize the theme with the final initialization flag, this ensures
     // that the theme is properly set even if it was initialized by calling
     // theme related function during bootstrap.
-    drupal_theme_initialize(TRUE);
+    drupal_theme_initialize();
     module_invoke_all('init');
   }
 }
diff --git a/includes/menu.inc b/includes/menu.inc
index 1fe5a64..60abab4 100644
--- a/includes/menu.inc
+++ b/includes/menu.inc
@@ -1777,7 +1777,7 @@ function menu_get_custom_theme($initialize = FALSE) {
  * Sets a custom theme for the current page, if there is one.
  */
 function menu_set_custom_theme() {
-  menu_get_custom_theme(TRUE);
+  return menu_get_custom_theme(TRUE);
 }
 
 /**
diff --git a/modules/simpletest/tests/custom_theme_boot_test.module b/modules/simpletest/tests/custom_theme_boot_test.module
index d89402e..20c8a64 100644
--- a/modules/simpletest/tests/custom_theme_boot_test.module
+++ b/modules/simpletest/tests/custom_theme_boot_test.module
@@ -14,10 +14,10 @@ function custom_theme_boot_test_custom_theme() {
     // the theme handling isn't right this will lead to a broken theme registry
     // and / or the wrong theme load.
     $node = node_load(arg(1));
-    if ($node->type == 'page') {
+    if ($node->type == 'page' && $node->promote) {
       return 'garland';
     }
-    elseif ($node->type == 'article') {
+    elseif ($node->type == 'article' && $node->promote) {
       return 'seven';
     }
   }
diff --git a/modules/simpletest/tests/custom_theme_boot_test.test b/modules/simpletest/tests/custom_theme_boot_test.test
index 67f1804..21e736f 100644
--- a/modules/simpletest/tests/custom_theme_boot_test.test
+++ b/modules/simpletest/tests/custom_theme_boot_test.test
@@ -41,6 +41,10 @@ class CustomThemeBootTestCase extends NodeWebTestCase {
       'type' => 'page',
       'promote' => 1,
     ));
+    $node3 = $this->drupalCreateNode(array(
+      'type' => 'page',
+      'promote' => 0,
+    ));
     $this->drupalLogin($this->admin_user);
     $this->drupalGet('admin/appearance');
 
@@ -56,13 +60,19 @@ class CustomThemeBootTestCase extends NodeWebTestCase {
     // custom_theme_boot_test.module. The implementation calls l() which again
     // end's up loading the theme.
     $this->drupalGet('node/' . $node1->nid);
-    $this->assertText('seven');
-    $this->assertNoText('garland');
-    $this->assertNoText('bartik');
+    $this->assertText('themes/seven/style.css');
+    $this->assertNoText('themes/garland/style.css');
+    $this->assertNoText('themes/bartik/css/style.css');
 
     $this->drupalGet('node/' . $node2->nid);
-    $this->assertText('garland');
-    $this->assertNoText('seven');
-    $this->assertNoText('bartik');
+    $this->assertText('themes/garland/style.css');
+    $this->assertNoText('themes/seven/style.css');
+    $this->assertNoText('themes/bartik/css/style.css');
+
+    // This makes sure that the base theme still loads as well.
+    $this->drupalGet('node/' . $node3->nid);
+    $this->assertText('themes/bartik/css/style.css');
+    $this->assertNoText('themes/garland/style.css');
+    $this->assertNoText('themes/seven/style.css');
   }
 }