The bonus is calculated on the base miles awared per flight and not for the actual miles given for the class of travel.

If you've had flights manually credited to your account it will depend when these were added as to when your bonus is credited. If they were flights in say May but not credited until July the bonus for these wouldn't have been credited until Aug. It's always automatic and should be never wrong. If you think it is drop me a email and i'll have a look.