How should flaps be used during an emergency landing (PPL)?
Specifically in your case you may have lost more altitude in the turn than your instructor or your turns were less coordinated etc. A wide variety of other variables that are hard to note with out accurate course data could have led to your outcome. You would have had to enter the maneuver at the same place/altitude to get similar results and the wind would have an effect here as well. Did you have a head wind or tail wind? Its worth covering some general procedures for this maneuver. 

When turning under glide its important to watch your airspeed and know how the plane will sink in a turn since you sacrifice some lift for the turn. 

Remember flaps allow you to make a steeper approach with out gaining airspeed but what that also means is your ground speed is effected (slowed). 

When it comes to the emergency landing procedure you are free to use flaps at your discretion and as mentioned its generally taught to use them once you are sure you have the field made. If the field is long enough you should shoot for a mid point incase you come up a bit short. Likewise if you are high you can go full flaps and slip it to lose altitude fast (if your instructor has not shown you how to slip a plane to lose altitude I would advise asking him to do so).