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?

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]