Seems to me that the biggest problem here is that you've written a P::RD grammer, which parses the Config file and produces a data structure to represent it. You then need to hand-roll your own parser to parse the output from P::RD in order to parse that into the format that you really want.

I realise that this isn't your fault. I spent some time reading the P::RD docs trying to work out how to get it to produce the format you want directly and save the second level of parsing. Whilst it may be possible, I gave up trying after many false starts and no apparent way to control the output format of P::RD.

This probably isn't what you want, but here's my take on the original problem of parsing this type of file. It use regexes and produces the required output in a single pass. No guarentees that it's complete or bullet proof, but I found this easier (by far) working out how to intervene in the P::RD process.

# perl -slw
use strict;
use re 'eval';
use Data::Dumper;

use vars qw[%Config];          # A global hash to contain the data

my $re_pair = qr{                  # key=value [[#;]comment text\n]
    (?{ our ($key, $value, $comment)=() })             # local vars

    (\w+) (?{ $key = $^N })            # Capture & save the keyname
    =
    (\w+) (?{ $value = $^N })            # Capture & save the value
    (?:
        \s+                                 # obligatory whitespace
        [#;]                      # oblig. comment card - either or
        ([^\n]+) (?{ $comment = $^N }) # Capture & save the comment
        \n
    )?                                                # zero or one
    \s*

          # If we got here, we have key/name comment?, so save them
    (?{ $Config{$section}{$key} = [ $value, $comment ] })
}x;

my $re_section = qr{                     # consist of [label] pairs*
    (?{ our ($section)=undef })                # Init the section labe
+l

    [[] ([^]]+) []]                              # Capture the label

                           # Save it. Create a key to hold the pairs
    (?{ $section = $^N; $Config{$section} = undef })

                # zero or more pair sounded by optional while space.
    \s* $re_pair* \s*
}x;

my $re_file =  qr{           # A file consists of 1 or more sections
    $re_section+
}x;

my $data = do{ local $/; <DATA> } . $/;             # slurp the file

$data =~ m[$re_file];                                     # parse it

print Dumper \%Config;                                      # Use it

__DATA__
[Section1]
key1=value1
key2=value2    #comment
key3=value3

[Section2]
key4=value4
key5=value5    ;Comment2

[Section3]
[download]

Output

$VAR1 = {
    'Section1' => {
        'key2' => [ 'value2', 'comment' ],
        'key1' => [ 'value1', undef ],
        'key3' => [ 'value3', undef ]
    },
    'Section3' => undef,
    'Section2' => {
        'key5' => [ 'value5', 'Comment2' ],
        'key4' => [ 'value4', undef ]
    }
};
[download]