diff --git a/includes/common.inc b/includes/common.inc
index 0437ec1..25e1e3a 100644
--- a/includes/common.inc
+++ b/includes/common.inc
@@ -5241,7 +5241,10 @@ function _drupal_bootstrap_full() {
     //   (e.g., hook_form_alter(), hook_node_view_alter(), hook_page_alter()),
     //   ahead of when rendering starts.
     menu_set_custom_theme();
-    drupal_theme_initialize();
+    // 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);
     module_invoke_all('init');
   }
 }
diff --git a/includes/theme.inc b/includes/theme.inc
index 8d5348d..d2fc40e 100644
--- a/includes/theme.inc
+++ b/includes/theme.inc
@@ -66,12 +66,17 @@ function _drupal_theme_access($theme) {
 
 /**
  * Initializes the theme system by loading the theme.
+ *
+ * @param bool $final_init
+ *   If enabled cache / static cache is cleared and the css / js files of the
+ *   theme are added to the output. This should only be used once after a full
+ *   drupal bootstrap.
  */
-function drupal_theme_initialize() {
+function drupal_theme_initialize($final_init = FALSE) {
   global $theme, $user, $theme_key;
 
-  // If $theme is already set, assume the others are set, too, and do nothing
-  if (isset($theme)) {
+  // If $theme is already set, assume the others are set, too, and do nothing.
+  if (isset($theme) && empty($final_init)) {
     return;
   }
 
@@ -97,7 +102,16 @@ function drupal_theme_initialize() {
     $ancestor = $themes[$ancestor]->base_theme;
     $base_theme[] = $themes[$ancestor];
   }
-  _drupal_theme_initialize($themes[$theme], array_reverse($base_theme));
+  // Initialize the theme but register the theme related css / js
+  // files just if the final initialization is requested.
+  _drupal_theme_initialize($themes[$theme], array_reverse($base_theme), '_theme_load_registry', $final_init);
+  if ($final_init) {
+    // Reset related caches that may have been built if the final initialization
+    // is requested.
+    drupal_static_reset('theme_get_registry');
+    $drupal_static_fast['registry'] = &drupal_static('theme_get_registry');
+    $drupal_static_fast['registry'] = array();
+  }
 
   // Themes can have alter functions, so reset the drupal_alter() cache.
   drupal_static_reset('drupal_alter');
@@ -137,70 +151,80 @@ function drupal_theme_initialize() {
  *    be first.
  * @param $registry_callback
  *   The callback to invoke to set the theme registry.
+ * @param bool $register_files
+ *   If enabled the css / js files of the theme are added to the output. This
+ *   shouln't be triggered before durpal isn't fully bootstrapped since this
+ *   could lead to a theme mix up if hook_custom_theme() is used.
  */
-function _drupal_theme_initialize($theme, $base_theme = array(), $registry_callback = '_theme_load_registry') {
+function _drupal_theme_initialize($theme, $base_theme = array(), $registry_callback = '_theme_load_registry', $register_files = FALSE) {
   global $theme_info, $base_theme_info, $theme_engine, $theme_path;
   $theme_info = $theme;
   $base_theme_info = $base_theme;
 
   $theme_path = dirname($theme->filename);
 
-  // Prepare stylesheets from this theme as well as all ancestor themes.
-  // We work it this way so that we can have child themes override parent
-  // theme stylesheets easily.
-  $final_stylesheets = array();
+  if ($register_files) {
 
-  // Grab stylesheets from base theme
-  foreach ($base_theme as $base) {
-    if (!empty($base->stylesheets)) {
-      foreach ($base->stylesheets as $media => $stylesheets) {
+    // Prepare stylesheets from this theme as well as all ancestor themes.
+    // We work it this way so that we can have child themes override parent
+    // theme stylesheets easily.
+    $final_stylesheets = array();
+
+    // Grab stylesheets from base theme
+    foreach ($base_theme as $base) {
+      if (!empty($base->stylesheets)) {
+        foreach ($base->stylesheets as $media => $stylesheets) {
+          foreach ($stylesheets as $name => $stylesheet) {
+            $final_stylesheets[$media][$name] = $stylesheet;
+          }
+        }
+      }
+    }
+
+    // Add stylesheets used by this theme.
+    if (!empty($theme->stylesheets)) {
+      foreach ($theme->stylesheets as $media => $stylesheets) {
         foreach ($stylesheets as $name => $stylesheet) {
           $final_stylesheets[$media][$name] = $stylesheet;
         }
       }
     }
-  }
 
-  // Add stylesheets used by this theme.
-  if (!empty($theme->stylesheets)) {
-    foreach ($theme->stylesheets as $media => $stylesheets) {
-      foreach ($stylesheets as $name => $stylesheet) {
-        $final_stylesheets[$media][$name] = $stylesheet;
+    // And now add the stylesheets properly
+    foreach ($final_stylesheets as $media => $stylesheets) {
+      foreach ($stylesheets as $stylesheet) {
+        drupal_add_css($stylesheet, array(
+          'group' => CSS_THEME,
+          'every_page' => TRUE,
+          'media' => $media
+        ));
       }
     }
-  }
 
-  // And now add the stylesheets properly
-  foreach ($final_stylesheets as $media => $stylesheets) {
-    foreach ($stylesheets as $stylesheet) {
-      drupal_add_css($stylesheet, array('group' => CSS_THEME, 'every_page' => TRUE, 'media' => $media));
-    }
-  }
+    // Do basically the same as the above for scripts
+    $final_scripts = array();
 
-  // Do basically the same as the above for scripts
-  $final_scripts = array();
+    // Grab scripts from base theme
+    foreach ($base_theme as $base) {
+      if (!empty($base->scripts)) {
+        foreach ($base->scripts as $name => $script) {
+          $final_scripts[$name] = $script;
+        }
+      }
+    }
 
-  // Grab scripts from base theme
-  foreach ($base_theme as $base) {
-    if (!empty($base->scripts)) {
-      foreach ($base->scripts as $name => $script) {
+    // Add scripts used by this theme.
+    if (!empty($theme->scripts)) {
+      foreach ($theme->scripts as $name => $script) {
         $final_scripts[$name] = $script;
       }
     }
-  }
 
-  // Add scripts used by this theme.
-  if (!empty($theme->scripts)) {
-    foreach ($theme->scripts as $name => $script) {
-      $final_scripts[$name] = $script;
+    // Add scripts used by this theme.
+    foreach ($final_scripts as $script) {
+      drupal_add_js($script, array('group' => JS_THEME, 'every_page' => TRUE));
     }
   }
-
-  // Add scripts used by this theme.
-  foreach ($final_scripts as $script) {
-    drupal_add_js($script, array('group' => JS_THEME, 'every_page' => TRUE));
-  }
-
   $theme_engine = NULL;
 
   // Initialize the theme.
diff --git a/includes/theme.maintenance.inc b/includes/theme.maintenance.inc
index 6baf219..6763257 100644
--- a/includes/theme.maintenance.inc
+++ b/includes/theme.maintenance.inc
@@ -71,7 +71,7 @@ function _drupal_maintenance_theme() {
     $base_theme[] = $new_base_theme = $themes[$themes[$ancestor]->base_theme];
     $ancestor = $themes[$ancestor]->base_theme;
   }
-  _drupal_theme_initialize($themes[$theme], array_reverse($base_theme), '_theme_load_offline_registry');
+  _drupal_theme_initialize($themes[$theme], array_reverse($base_theme), '_theme_load_offline_registry', TRUE);
 
   // These are usually added from system_init() -except maintenance.css.
   // When the database is inactive it's not called so we add it here.
diff --git a/modules/simpletest/simpletest.info b/modules/simpletest/simpletest.info
index 7b139ba..0866f60 100644
--- a/modules/simpletest/simpletest.info
+++ b/modules/simpletest/simpletest.info
@@ -14,6 +14,7 @@ files[] = tests/batch.test
 files[] = tests/bootstrap.test
 files[] = tests/cache.test
 files[] = tests/common.test
+files[] = tests/custom_theme_boot_test.test
 files[] = tests/database_test.test
 files[] = tests/entity_crud.test
 files[] = tests/entity_crud_hook_test.test
diff --git a/modules/simpletest/tests/custom_theme_boot_test.info b/modules/simpletest/tests/custom_theme_boot_test.info
new file mode 100644
index 0000000..3b1d2dd
--- /dev/null
+++ b/modules/simpletest/tests/custom_theme_boot_test.info
@@ -0,0 +1,6 @@
+name = Custom theme boot tests
+description = A support module for custom theme hook boot testing.
+core = 7.x
+package = Testing
+version = VERSION
+hidden = TRUE
diff --git a/modules/simpletest/tests/custom_theme_boot_test.module b/modules/simpletest/tests/custom_theme_boot_test.module
new file mode 100644
index 0000000..d89402e
--- /dev/null
+++ b/modules/simpletest/tests/custom_theme_boot_test.module
@@ -0,0 +1,37 @@
+<?php
+/**
+ * @file
+ * Helper module for the custom theme boot tests.
+ */
+
+/**
+ * Implements hook_custom_theme().
+ */
+function custom_theme_boot_test_custom_theme() {
+  if (arg(0) == 'node' && is_numeric(arg(1))) {
+    // This triggers a node load - which again could trigger a whole bunch of
+    // theme related stuff e.g. by triggering token replacement in fields. If
+    // 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') {
+      return 'garland';
+    }
+    elseif ($node->type == 'article') {
+      return 'seven';
+    }
+  }
+}
+
+/**
+ * Implements hook_entity_load().
+ */
+function custom_theme_boot_test_entity_load($entities, $type) {
+  if ($type == 'node') {
+    foreach ($entities as $entity) {
+      // This is going to initialize the theme and break everything if not
+      // properly handled.
+      $entity->foo = l(t('foo'), '');
+    }
+  }
+}
diff --git a/modules/simpletest/tests/custom_theme_boot_test.test b/modules/simpletest/tests/custom_theme_boot_test.test
new file mode 100644
index 0000000..67f1804
--- /dev/null
+++ b/modules/simpletest/tests/custom_theme_boot_test.test
@@ -0,0 +1,68 @@
+<?php
+/**
+ * @file
+ * Helper module for the custom theme boot tests.
+ */
+
+/**
+ * Tests for custom theme boot behaviour.
+ */
+class CustomThemeBootTestCase extends NodeWebTestCase {
+  protected $profile = 'testing';
+
+  public static function getInfo() {
+    return array(
+      'name' => 'Custom theme boot tests',
+      'description' => 'Test that triggering custom theme on boot wont compromise the theme registry.',
+      'group' => 'Theme',
+    );
+  }
+
+  public function setUp() {
+    parent::setUp('custom_theme_boot_test');
+    // Create and login admin user.
+    $this->admin_user = $this->drupalCreateUser(array(
+      'access administration pages',
+      'administer site configuration',
+      'administer themes',
+    ));
+  }
+
+  /**
+   * Create four nodes and ensure they're loaded correctly.
+   */
+  public function testNodeMultipleLoad() {
+    // Create nodes to fetch.
+    $node1 = $this->drupalCreateNode(array(
+      'type' => 'article',
+      'promote' => 1,
+    ));
+    $node2 = $this->drupalCreateNode(array(
+      'type' => 'page',
+      'promote' => 1,
+    ));
+    $this->drupalLogin($this->admin_user);
+    $this->drupalGet('admin/appearance');
+
+    // Enable Garland theme.
+    $this->clickLink('Enable');
+    // Enable Seven theme.
+    $this->clickLink('Enable');
+
+    // Clear all caches.
+    cache_clear_all();
+
+    // Fetch the node. This triggers hook_entity_load(), which is implemented by
+    // 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->drupalGet('node/' . $node2->nid);
+    $this->assertText('garland');
+    $this->assertNoText('seven');
+    $this->assertNoText('bartik');
+  }
+}