I found the problem! Here's how to get the minion: Do all the quests the Moogle gives you but you also have to have this completely random sidequest done:

Doing the Dirty Work by Marcette
Central Shroud -Sorrel Haven (16,18)

He gave me other quests at first too, apparently I had not done them either but once Doing the Dirty work appeared and I did it, and went back to Limsa, the Moogle was back! ^.^