"Character’s who take levels in their favored class can also choose to gain 1 additional skill point". Does this bonus apply EVERY time a character takes a level in their favored class?
Yes...
Since humans already effectively gain this bonus and their favored class is "any", do these bonuses stack to basically double their normal bonus as long as they don't multiclass?
No.From the book:
Favored Classes
Each race has two favored classes, representing its natural affinity for a specific set of skills and abilities. Whenever you take a level in your race’s favored class, you receive either +1 hit point or +1 skill point. Humans and half-elves frequently get this bonus, unless they multiclass. You do not gain this bonus for taking levels in a prestige class, regardless of its theme.
Favored Class: Humans can choose any one class as
their favored class at 1st level. Once made, this choice
cannot be changed.
So, the humans can choose two favored class, at 1st level and this chocice cannot be changed.
Wait, i dont fully understand what you´re meaning with