Custom story not working after installing justine

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As I said it worked before I installed justine... and I didn't change anything since then

That is the current problem: you need to change (correct) things in your full conversion. The Justine patch does more than merely install a few new maps, entities, static objects, etc. In fact, i'm inclined to say that full conversions became popular because of the Justine patch. Of course, if you don't want to compare and contrast your set up with the tutorial linked to you and decide to uninstall the patch (possibly even reinstall the game) and leave things as is, that is fine. However, i should mention a lot of people have the Justine patch installed on their system.