It appears that in some cases upsertGraph isn't inserting rows. Example:

My Preferences model was set up with table.primary(['userId', 'category']) and below is what I'm trying:

const prefs = [{ category: 'sms', setting: 'off' }, { category: 'sound', setting: 'off' }];
Users.query().upsertGraph({ id: user.id, preferences }).asCallback((err, updated) => {

    console.log(updated);
});

Will log:

Users {
  id: 23,
  preferences: 
   [ Preferences { category: 'sms', setting: 'nope', userId: 23 },
     Preferences { category: 'loudNoises', setting: 'nope', userId: 23 } ] }

If there's nothing in the table, then adding a debug() to the builder chain will show that 2 selects are being generated, but no insert/updates. If there's data in the table, anything not contained in the preferences array will be deleted, but nothing gets inserted.

It could be that, because we already have the primary key (['userId', 'category']) it's not trying to do the insert but because the row doesn't exist, it's not trying to update?