[eluser]Jumper[/eluser]
My specific problem is that I set (for various reasons) the $config["site_url"] inside a separate auto-loaded config file.
And since it is not loaded automatically, the cache get broken, because it depends on correct $config['site_url'] .
I temporarily solved this by modifying Codeingiter.php to autoload needed config files before using the cache, but I hope to get a more standard solution