It doesn't mean the loop "isn't working" at all; only that the results aren't what you were expecting. The problem is likely the data are zero elsewhere.
It isn't possible to diagnose anything without sample data and it's certainly not clear what the real underlying intent of the code is, but it looks most peculiar.
Reduce the problem size to one that is manageable to see what is going on (an 8-10 x 10-20 array is just as useful to test code logic as is something huge and yet is small enough that one can inspect the input and output to find out where the logic issue(s) is(are).
