permalinks are not working at all
you have to manually update the qtranslate.php to fix this - I had the same problem, that as soon as I activated the plugin, everything was giving a 404 error, and I couldn't access the control panel in order to change any settings. Go into the plugins page, and edit qTranslate - then set $q_config['hide_untranslated'] to false. I assumed that because I didn't have any translations yet, or even any content, every page was being hidden. So you need to unhide untranslated pages.
