Honestly, I'm not 100% sure what's going on, but there is something you might want to try. I had an issue with Kapalla where her second dungeon event would just not trigger. I tried several levels of Malgrid, easily 5-6 runs and it just wouldn't pop up. So, I did a normal mission with her (Dragon Slayer, since it's long and has no map-to-map events of its own) and guess what? At the last map transition, the event finally popped up.
I guess there might be an issue with the mechanic that triggers the dungeon events in Malgrid. Maybe the piece of code that blocks you from cheesing all events at once by just going back and forth between two map nodes to trigger events starts to go crazy and blocks the events there altogether. So, maybe give it a try with any long, non-Malgrid mission like Dragon Slayer. It worked to fix the issue for me.