Way of the Tempest completely broken?

So I went to pick up my specilization quest, and when it started I already had 2/3 Essence Containtment Apparatuses and 3/3 Spirit Essences.  Great, I thought, this shouldn't take very long.  Except despite having 3/3 Spirit Essences, it didn't count that as completed.  And when I finally figured out where to get my 3rd Esence Containment Apparatus, it didn't count that as completed either.  So now I'm just stuck in limbo and can't go with the specialization.

All the specialization quests were partially done when I picked him up, so I'm assuming I won't be able to do any of them.

So yeah, what now?  Seems like I'll be missing out on a pretty major part of the game.