Presuming you are on AFPS75 you get the daily PAS pension supplement for every day served on the old scheme to the day of transition. From that point the entire salary is used for the AFPS15 calculation.
Whilst this quote is listed on the calculator:
5. Those specialist groups that attract pension supplements will have their supplements based on actual days served up to the point of transition to AFPS 15 - in accordance with current rules for their specialism.
I am not entirely convinced it works correctly for all scenarios.