Well, that is easy enough, just change one line in the code I posted:

$C{$y}=$aoa->[1];

# to

$C{$y}=[@$aoa[1..$#$aoa]];

__OUTPUT__
$VAR1 = {
          'Section1' => {
                          'key2' => [
                                      'value2',
                                      '   #Comment2'
                                    ],
                          'key1' => [
                                      'value1'
                                    ],
                          'key3' => [
                                      'value3'
                                    ]
                        },
          'Section2' => {
                          'key5' => [
                                      'value5'
                                    ],
                          'key6' => [
                                      'value6',
                                      '   ;Comment 6'
                                    ],
                          'key4' => [
                                      'value4'
                                    ]
                        }
        };
[download]

Thanks