Make sure you're using "Compile to Flash, run in RAM" when you compile your program to the board. If you just use "Compile to RAM", it won't work.
If you're already doing that, can you test with one of the simpler sample programs to see if it's something specific about your program that's failing? Do you have any printf() output? If so, you can use the macros described in Samples/SERIAL_STDIO.C to redirect that output to serial port A, and use the DIAG connector of the programming cable to monitor your program.