Updated the game, issue persisted. I couldn't find the button to restart the SE so (after some testing with the original rom to see if that one maybe was modified without my knowledge (it wasn't)) I just decided to fight the Giratinas instead. A few reviver + stun seeds did the trick.
Am a bit concerned about proceeding with my current save file though, I only started playing the SEs yesterday on the patch from the 24th, so maybe my entire save is f-ed because I started playing on 1.1 and I won't see some new content...
Speaking of which, in a previous reply you said early evolution would be possible in 1.2, how early are we speaking? Because I couldn't evolve my starters after unlocking the spring (on 1.2), which seems to be the usual trigger for early evo.