If the appointment is less than 24 hours out from the time set then the alerts will reverse.
Example Appointment is set for January 1, 2014 at 10:00 pm. You are setting it on 12/31/13 at 11:00 pm. You want Alert 1 to be 24 hours ahead and Alert 2 to be 5 mins before. The calendar app will automatically put the 5 mins before Alert as Alert 1. The reason is because your appointment is occurring less than 24 hours away.
The Appointment must be at least 24 hours out or more.