#!/usr/bin/perl

use strict;
use warnings;
use diagnostics;
use Data::Dumper;

my $Messages = {
    
        '21:32:15.111' => ["233.156.208.11:2004", "214111"],      # Us
+ing the Time Stamp as a key
        '21:32:15.222' => ["233.156.208.22:2004", "214222"],      # to
+ an anonymous array containing
        '21:32:15.333' => ["233.156.208.33:2004", "214333"],      # mi
+lliseconds and "Pending Number".

        };
        
print Dumper($Messages);                                          # Us
+ed to check the contents of your variables.

__END__

$VAR1 = {
          '21:32:15.222' => [
                              '233.156.208.22:2004',
                              '214222'
                            ],
          '21:32:15.111' => [
                              '233.156.208.11:2004',
                              '214111'
                            ],
          '21:32:15.333' => [
                              '233.156.208.33:2004',
                              '214333'
                            ]
        };
[download]

A few other things I noticed that you may want to review:

while ( $line = <LOG> ) {
unless (($data[10] =~ m/Pending=/) || ($data[6] =~ m/Gap/)) { next; } 
+# skip elements we don't want
     if ($line =~ m/Pending=/) {
        my @data=split(/ /,$line); # split the line up
        $data[10] =~ s/[A-Za-z=.]//g; # delete "Pending", "=" and "."
        $data[1] =~ s/\..*//g; # delete the millisecond element of the
+ (line)lTime var
        my @lTime=split(/:/,$data[1]); # split the line time
        my $lSecs=$lTime[0] * 3600 + $lTime[1] * 60 + $lTime[2]; # con
+vert line-time to seconds

        if (($data[0] eq $ymd) && ($data[10] >= $tHold) && ($lSecs >= 
+$sSecs) && ($lSecs <= $eSecs))
            {
                   $line = "$data[1],$data[10]";
                }
   }
[download]

I — think — you may be trying to load each line of the file into an array, then match the records you want? (I don't think you need to start out trying to skip unwanted lines. Just match what your looking for from the start.) In terms of your regex matches you could possibly use something like:

m/(?:Pending=)(\d{6})$/ # If you want the number after 'Pending'.

m|\s(\d\d:)+(\d){2}\.(\d){3}\s| # To match the time stamp.
[download]

These are just some ideas but if you could possibly provide a little more clarity that will help much smarter monks help you. :)