1. Right out of the box, if you create a extended or classic 
application, with all the default settings and default device, and run 
it, at the point where the APDUTool is suppose to start sending the 
APDUs to the card, it just says connected and gets stuck there. The 
problem there is basically that protocol difference between the cjcre 
and the apdutool. I looked in the configuration file for the default 
device, and saw that it had t=0 set for the apdutool. Going in and 
changing that in the customization window for the default device, fixes 
the problem.

2. Any changes that you make in the customization dialog box after 
creating the default platform don't have any effect to the configuration 
of the device. I tried it multiple times with protocols, memory sizes 
etc., the changes never showed up in the configuration file or have any 
effect on the actual running of the device.