So a bit of an update, I did manage to eventually force it to work, It did require a number of new games before I could get passed the stick.
I think it's not detecting the relic being collected properly, which I believe is what allows you to leave the first farm area.
Would a solution be to redesign that fixed map, making it so after the 'boss' fight that you 'collect' the item as you leave ? or trigger a cutscene after the lockpick minigame ?