FibonacciElement.cmp is OK. Quoting from the book (end of 8.3.1)
... the computer's bootstrap code should effect the following operations (in machine language):
    SP=256          // Initialiaze the stack pointer to 0x0100
    call Sys.init   // Start executing (the translated code of) Sys.init
 
 
That's a 
VM call, not just a jump.
When Sys.init() starts runing, there is a full stack frame on the stack. This stack frame is why the final SP is 5 greater than you are expecting.
--Mark