Clearly the mechanism that contributes to the electrostatic build-up in a thunderstorm is not completely understood. There are a few methods that appear to contribute and additional knowledge remains to be better understood.  One of the methods considered important is the electrostatic discharge from the  snap freezing process.

Supercooled water video.  another (better) Supercooled water video    Cloud droplet    
 Charge Separation    More about "Snap Freezing and the charge"

Another method is the electrostatic charge from falling drops of water as describe by Lord Kelvin in the 1800's. Lord Kelvin gave us a clue on how one of the charge mechanisms may work in the thunder cloud. 

This water drop demonstration will show the rapid build up of an electrostatic charge with a few drops of falling water.  I have measured a 20,000 volt charge with as few as 110 drops of water through each side in less than six seconds.  As you can imagine, the charge build is quite exponential.   Watch video here  wmv file 5.3 Meg

More on the subject from Bill Beaty             Bill's in-line version 

Additional sources  on the subject of how lightning works and how it is generated:

http://www.ce-mag.com/archive/02/09/mrstatic.html

http://www.ce-mag.com/archive/02/07/mrstatic.html

http://www.ce-mag.com/mrstatic.html