Calibrating/Correctly draining an Extended Battery
Firstly, battery calibration is a myth, normal or extended battery. See Bought a new battery, do I need to calibrate it?
Next, with extended batteries, there is always a possibility that the correct capacity of the battery is not being read  by the ROM and displayed ( since there are two different sources for reading the battery capacity and it may be reading from the hardcoded (ROM) rather than battery capacity files. See for more details here Where are the battery capacity files located?)


What you can do


Measure the actual capacity of your battery as explained here How to determine maximum capacity of a battery in mAh? - received fake battery using the app mentioned. 
Adjust the capacity of the battery manually in the app (from Battery Manager → Tap the 4 small square icon → Adjust Capacity or use Configuration Wizard) and create a shortcut on your home screen for the Battery Mgr widget and use that to measure


You can optionally avoid the first step above if you trust the battery provider capacity and adjust on the app