Alright, just an update. I believe I have found the problem.

use strict;
use Data::Dumper;

my $start = {};

sub add{
    my $root = shift;
    my $level = shift;
    my @items = @_;
    if(!@items) {return $level-1;}
    #print "level = $level\n";
    while(@items) {
        my $first = shift @items;
        $root->{$first}->{count}++;
        if(!exists($root->{$first}->{children})) {$root->{$first}->{ch
+ildren}={};}
        #print "\t" x $level . "first = " . $first . ", values = " . j
+oin(',',@items)."\n";
        $root->{$first}->{max} = add($root->{$first}->{children}, $lev
+el+1, @items);
    }
}

add($start, 1, 1..4);
add($start, 1, 1..2);

print Dumper($start);
[download]

I was passing hash reference that were undefined, which is not a good thing apparently. So, I fixed that problem.