Here is the revised version of the code, which now keeps the windows up:

  $filename="log3.txt";
  open(TXT, $filename)||die("Could not open file!");
  @filedata = <TXT>;
  close TXT;
  close TXT;
  open (TXT, ">$filename");
  
  @alert = ['a'..'z'];
  $i=0, $p=1;

  while(@filedata || !@filedata)
  {
      if($filedata[0] =~ /(\s+)(\d{1,4})(\.\d{1,4}){3}(\s+)/)
      {
          &Build_Window;
      }
      shift(@filedata);
      ++$i; ++$p;

    if(!@filedata)
    {
        open(TXT, $filename)||die("Could not open file!");
        @filedata = <TXT>;
        close TXT;
        open (TXT, ">$filename");
        close TXT;
        &Loop;
    }
  }
  Win32::GUI::Dialog();


sub Loop
{
      if($filedata[0] =~ /(\s+)(\d{1,4})(\.\d{1,4}){3}(\s+)/)
      {
          &Build_Window;
          Win32::GUI::Dialog();
      }
      shift(@filedata);
      ++$i; ++$p;

    if(!@filedata)
    {
        open(TXT, $filename)||die("Could not open file!");
        @filedata = <TXT>;
        close TXT;
        open (TXT, ">$filename");
        close TXT;
        &Loop;
    }
}
  
sub Build_Window
{
        $datetime = localtime();
        $alert[$i] = new Win32::GUI::Window(-name => "Alert", -width =
+> 500, -height => 150, -pos => [$p*2, $p*2]);
        $font = Win32::GUI::Font -> new(-name => "Arial", size => 46, 
+-bold => 1);
        $alert[$i] -> AddLabel(-text => $datetime, -font => $font);
        $alert[$i] -> AddLabel(-text => "SNORT ALERT: MALICIOUS BEHAVI
+OR DETECTED!", -font => $font, -top => 50);
        $alert[$i] -> AddLabel(-text => $filedata[0], -font => $font, 
+-top => 75);
        my $t1 = $alert[$i] -> AddTimer('T1', 1000);
        Win32::Sound::Play("SystemExclamation");
        $alert[$i] -> Show();
        Win32::GUI::Dialog();

        sub T1_Timer { return -1; }
        sub Alert_Terminate { return 1; }
}
[download]

The problem I have now is that only the first set of windows (the data that was first wrote to the log file) appears. Does anyone have any thoughts on this?

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.

---

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

"Science is about questioning the status quo. Questioning authority".

In the absence of evidence, opinion is indistinguishable from prejudice.

"Too many [] have been sedated by an oppressive environment of political correctness and risk aversion."

Try putting a sleep(10) after BrowserUK's suggestion to see if windows really do come back. If that works, then you need to put a Window up that asks a question and waits for a user response. I'm not familiar with the particular module that you are using, but for example with Win32::MsgBox (I didn't worry about import of specific constants, etc).. just the basics .....

use Win32;
my $ERROR_OK_BOX=16;        # Red Error X box with an ok button

Win32::MsgBox("Some errors deteted, click Ok to end program", 
               $ERROR_OK_BOX,"some_title"  );
print "program now exiting\n";
[download]