I've been feeling pretty sure that I've flipped around through CRB enough to run up on everything I'm due, but it was only a few days ago that I discovered the Favored Class Bonus to either hp or skill ranks, so I'm totally open to there being something hiding around in there somewhere!
This was my first attempt at using VentureCaptain, which I was considering trying as a hopefully easier way of making bunches of characters for my players, but I think what's happened is that I've discovered it not to be trusted.
Very much appreciated, yall!