It looks to me like bbqquery is confused about the modifiers on inner classes. If I ask for "package all classes", it gives me private and package inner classes. If I ask for "private all classes", or "protected all classes", I get nothing. "static all classes" gives me nothing, either.
Easy to reproduce; just create a class, and give in inner classes with the appropriate modifiers.
I haven't seen the problem with top-level classes.