That's actually working properly. To get a spawn for a boss (which is Expedition #5), you are asked to turn in your grimoire, and upon finishing (either winning or losing) the expedition, you're given a fresh grimoire with no progress on it. It's just how Meebles works. You work up a tier and get to the boss, then start at a new tier, repeat. The only thing that carries over are clears for reward purposes (all Rank 3s, etc) and KIs won from bosses (which are lost when you get a spawn for the overall zone boss).

Edit: Sniped. Beaten to it.