"Stijn,
ArduCopter 3.3's EKF does not use GPS's altitude. It uses the barometer's altitude instead. Could you please tell more how the GPS's altitude is used?"
"These changes introduced a delay (negative or positive) between _last_GPRMC_ms and state.last_gps_time_ms. This delay depends on the baud rate, and also probable depends on the order of the messages."