# shuffle - I'll do it in pure perl.
[download]

Too bad your implementation is flawed:

use strict;
use warnings;

my $size  = 4;
my @array = 1 .. $size;
my %count;

foreach (1 .. 24_000) {
    my @sample = @array;
    my $i = $size;
    while ($i--) {
        my $j = int rand($i);
        @sample[$i, $j] = @sample[$j, $i];
    }
    $count {"@sample"} ++;
}

foreach my $key (sort keys %count) {
    printf "%s: %4d\n", $key, $count {$key}
}

__END__
2 3 4 1: 3999
2 4 1 3: 4029
3 1 4 2: 3969
3 4 2 1: 4000
4 1 2 3: 4031
4 3 1 2: 3972
[download]

In stead of getting 24 different permutations, each appearing about 1,000 times, your algorithm produces only 6 permutations, each appearing about 4,000 times.

Better use a module next time!