"some of the associated records were not loaded" but they are

I use Ember.js in something of an untraditional way, where I prefer to load everything I could want in my routes, and then switch my relationships to async: false

However, I've recently run into a peculiar issue, where I am updating a relationship on a model, then pushing the updated record into the store. In most cases, it works, but in this case I'm getting the "some of the associated records were not loaded" error, which is particularly bizzare, since they are definitely loaded.

It seems like ember.js just isn't linking them up properly during the store.push? Does anyone have any insights?