I never found out what was causing it, so if you figure it out, let us know!
I wager it's something cosmetic I was doing to my character, since I had a preset customization I was pasting in from several versions ago. I really have no idea, though. On a final run of the game, I opted to just grab Puppet first while doing as little as possible of anything else.
Fortunately, besides providing you with an early Bone Lance, it's not a very great companion, it just looks cool. You're not necessarily missing much if you don't get it.