Confused about a bit of code.

http://pastebin.org/121306

Could a friendly soul explain to me why removing/changing the for-loop at line 68-69 changes the whole program?
It changes output from   1 2 3 4 5   to   3 2 1 5 4 
if the input is 5 4 3 2 1

>>2
Well, removing it entirely changes the behaviour into what I described up top.
If I change it to for example only go to A.length - 2, then it prints out something like 22354

But I don't understand why it has any effect on the return output? :/

>>4
What about lines 61-62?