You'd get better responses if your code showed some semblence of effort. A few questions:

1. Why are you initialising @alerts with an anonymous array containing the characters 'a'..'z'?
2. Why do you have two subroutines embedded within a subroutine?
3. What it sub T1_Timer() meant to achieve?
4. Why aren't you using strict?
5. How is sub Loop() ever meant to be run?
6. Why are you closing the file twice?
7. Why do you then reopen it for output and never close it?

Anyway, try this:

#! perl -slw
use strict;
use Win32::GUI();
use Win32::Sound;

my $filename="yourfile.dat";
open(TXT, $filename)||die("Could not open file!");
my @filedata = <TXT>;
close(TXT);

my( $running, @alerts ) = 0;
my $p = 100;

for my $element ( @filedata ) {
    if( $element =~ /(\s+)(\d{1,4})(\.\d{1,4}){3}(\s+)/) {
        push @alerts, Build_Window( $element, $p += 10 );
        ++$running;
    }
}

sub Alert_Terminate { return --$running ? 1 : -1; }

sub Build_Window {
    my( $element, $pos ) = @_;

    my $win = new Win32::GUI::Window(
       -name => "Alert", -width => 500, 
       -height => 150, -pos => [ $pos, $pos ]
    );
    my $font = Win32::GUI::Font->new(
       -name => "Arial", size => 46, -bold => 1
    );
    $win->AddLabel(-text => localtime(), -font => $font);
    $win->AddLabel(
        -text => "SNORT ALERT: MALICIOUS BEHAVIOR DETECTED!", 
        -font => $font, -top => 50
    );
    $win->AddLabel(-text => $element, -font => $font, -top => 75);
    Win32::Sound::Play("SystemExclamation");
    $win->Show();
    return $win;
}

Win32::GUI::Dialog();
[download]

But be aware, your apparent lack of understanding, and of effort to understand, means that you are going to have to start reading some documentation, and try to develop your understanding by writing a few simple (non-GUI) programs, before you will get further help from me.