No, you're not getting the output you show using the JSON you posted. Look at the #@%!^ JSON you posted. It is not capable of resulting in the output you are showing. Here's what I get when I test it:

use strict;
use warnings;
use File::Slurp;
use JSON;

my $json = read_file(\*DATA);

my $j = JSON->new;

my %json_text = %{ $j->decode($json) };

while( my ( $key, $value ) = each %json_text ) {
  print "$key = $value\n";
}



__DATA__
{
   "alertCounts" : [
      {
         "count" : 5,
         "rule" : "rule1"
      },
      {
         "count" : 16,
         "rule" : "rule2"
      }  
   ],
   "balArray" : [
      {
         "containerArray" : [],
         "name" : "user_ip"
      },
      {
         "containerArray" : [
            {
               "entryArray" : [
                  {
                     "action" : "flag",
                     "expires" : "00:00:00",
                     "hitsSinceAdded" : 56,
                     "name" : "/my/page",
                     "priority" : 4,
                     "rule" : "rule1",
                     "timestamp" : "15:28:40.150"
                  }
               ],
               "name" : "192.168.1.100"
            },
            {
               "entryArray" : [
                  {
                     "action" : "flag",
                     "expires" : "00:00:00",
                     "hitsSinceAdded" : 185,
                     "name" : "/my/page",
                     "priority" : 4,
                     "rule" : "rule2",
                     "timestamp" : "15:12:55.961"
                  }
               ],
               "name" : "192.168.1.101"
            }
[download]

And the output:

, or ] expected while parsing array, at character offset 1206 (before 
+"(end of string)") at ./mytest.pl line 12.
[download]

I don't know how many more times you need someone to tell you that the sample input you're posting isn't capable of producing any reasonable output because it's broken. Post real JSON that isn't malformed, and we can begin to talk about your code.