The old version uses PIC-Microcontroller, the new one ATMEL!! THESE ARE TWO COMPLETELY DIFFERENT COMPONENTS!
Never try to flash one of the old PICs with the new board and vice versa.... this will not work
Once programmed, you can use the old modules with the new com-board, but I guess best is not to mix them up....
Programming the Hardware of the new system is completely different from the first generation, always think of that!
regards