Tex,
The Flight Timer is based on several flight parameters and can sometimes be off a little, example taxi time, slow flight, GPS signal loss, etc. There are some known accuracy issues that we need to iron out on this feature. Stay tuned for this in a future update.
There are also some planned improvements to the Timer function as well as adding "User Defined Alarms" for tasks like Switching Tanks, Re-Fuel, procedures, countdown, etc. These are on our internal development and wishlist for future updates.