Index: branches/5.3.x/core/kernel/utility/unit_config_cloner.php
===================================================================
--- branches/5.3.x/core/kernel/utility/unit_config_cloner.php
+++ branches/5.3.x/core/kernel/utility/unit_config_cloner.php
@@ -66,16 +66,17 @@
 	/**
 	 * Creates unit configs, based on 'Clones' option.
 	 *
-	 * @param string $prefix Unit config prefix.
+	 * @param string  $prefix      Unit config prefix.
+	 * @param boolean $with_cached Process also cached clones.
 	 *
 	 * @return array
 	 */
-	public function extrude($prefix)
+	public function extrude($prefix, $with_cached = true)
 	{
 		$main_config = $this->reader->getUnitConfig($prefix);
 		$sub_configs = $main_config->getSetting('Clones', array());
 
-		if ( isset($this->clones[$prefix]) ) {
+		if ( $with_cached && isset($this->clones[$prefix]) ) {
 			$sub_configs = array_merge($sub_configs, $this->clones[$prefix]);
 		}
 
Index: branches/5.3.x/core/kernel/utility/unit_config_reader.php
===================================================================
--- branches/5.3.x/core/kernel/utility/unit_config_reader.php
+++ branches/5.3.x/core/kernel/utility/unit_config_reader.php
@@ -478,7 +478,8 @@
 			$this->runAfterConfigRead($preloaded_prefix);
 		}
 
-		$clones = $this->cloner->extrude($preloaded_prefix);
+		// Only use cached clones for calls in the middle of initialization (e.g. url parsing).
+		$clones = $this->cloner->extrude($preloaded_prefix, !$this->finalStage);
 
 		if ( $this->finalStage ) {
 			foreach ( $clones as $a_prefix ) {