Hi,
I can not explain why the application 1 is working and not the second.
The question is: are you sure that the application is is really downloaded via the bootloader ?
To check it I suggest you to create another application for instance the default EVM application (led blinking).
Load this application on board.
Now the bootloader is erased.
Reload the bootloader and try to load the application 1.
is it working ?
Try the same with the application 2. is it working ?
If you still have he problem, can you check if the application 2 is working in debug (via CodeWarrior debugger) ?
What is the tool version used ?
Regards
Pascal