@reddo: I meant that the same link now has new version, which you could try too.
Plugin "qTranslate Menu Item" is not on repository anymore. Could you send it to me to qtranslateteam at g m ail d com?
it's got 30-ish items.
Have you set your max_input_vars as described at the bottom of https://qtranslatexteam.wordpress.com/troubleshooting/ ?