We'd need to see the code where you create your hash to know what your problem is. This seems to work as I would expect:

#!/usr/bin/perl -w

use strict;
use Data::Dumper;

my %data = ( A => { one => 1,
                    two => 2,
                    three => 3 },
             B => { four => 4,
                    five => 5,
                    six => 6 },
             C => { seven => 7,
                    eight => 8,
                    nine => 9 } );

print Dumper(\%data);
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The output is:

$VAR1 = {
          'A' => {
                   'three' => 3,
                   'one' => 1,
                   'two' => 2
                 },
          'C' => {
                   'nine' => 9,
                   'eight' => 8,
                   'seven' => 7
                 },
          'B' => {
                   'six' => 6,
                   'five' => 5,
                   'four' => 4
                 }
        };
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