Could you possibly have meant:

for (my $i = 0; $i <= 4; $i++) {
  my $j=0;
  while (my $line = readline(SORTD)) {
    $j++;
    my $number = substr($line, $j*2, 2);
  }
}
[download]

Just a wild guess of course but when you wanted the counter of the inner loop to vary, you probably meant to have a different variable.

(There are nicer ways of writing this but I wanting the changes to be obvious.)