Its been awhile since I generated an exe with GUI on Windows - the last major release was on XP. The default was a command line task that shows STDOUT/STDERR and then a task for the GUI itself (much bigger).

With PerlApp, there was an option to eliminate this extra task that when maximized shows command line output. I guess that you are using pp? I suspect that there is a similar "launch option". If there is not, then it is possible to write some Perl code to launch your app as a "detached process", meaning that there is no command line. From my previous testing this is about 1/2 page of Perl. Look for a compile option in pp. From my memory on WinXP, killing the command line task also killed the GUI. Windows is a complicated beast - I have no idea why that doesn't work on Win10.

Update:
I was trying to kill my application from outside Perl (to perform an update which requires my application to be killed)
I can't even imagine intentionally doing such a thing. My gosh you are describing something that would be a program crash! I mean as a user if I'm using the GUI and then all of a sudden "poof", the program dies, I'd be pretty upset!! Internally within the main application code, a "kill" command from the OS will likely cause some data loss.

I have tested Perl signal handlers under Windows - I don't remember exactly how, but there has got to be some better way for your update process to work. Issuing a "kill" at a random moment during user GUI interaction is "BAD, VERY BAD".

Update:
If you don't want the command line task, something similar to this should work. I got this from one of my Perl books and I remember testing something close to this in the past. This code does appear in a copyrighted book, but it is so short that I think "fair use" applies because it just shows how to use Win32::Process::Create().

#!/usr/bin/perl -w
# loader - starts Perl scripts without the annoying DOS window
use strict;
use Win32;
use Win32::Process;

# Create the process object.

Win32::Process::Create($Win32::Process::Create::ProcessObj,
    'C:/perl5/bin/perl.exe',            # Whereabouts of Perl
    'perl realprogram',                 #
    0,                                  # Don't inherit.
    DETACHED_PROCESS,                   #
    ".") or                             # current dir.
die print_error(); #or perhaps, just die "some error msg";
#consider using the START command in a Windows batch file

sub print_error() {
    return Win32::FormatMessage( Win32::GetLastError() );
}
[download]