How are you testing for a stall? It looks to me as if it may be difficult to correctly detect a stall condition with the current DifferentialPilot code. I will raise this with the other devs. Looking at the code it would seem that when a stall is detected then the current move operation is aborted (by calling stop, so there is probably no need for you to call quickStop in this case), so one way would to detect a stall might be to wait for a move to complete and then to check if the end position is what you would expect it to be.
If you want to understand how something works you can always take a look at the source code. This will have been installed on your system as part of the standard install, or you can browse the source on line. Here is the latest version of DifferentialPilot:http://lejos.svn.sourceforge.net/viewvc ... iew=markup
As you can see quickStop, changes the acceleration used and then calls stop...