After much trial and error, I came up with this snippet. As always, YMMV.

Create a sample popup window:

# popup.pl
use Win32;

Popup('testing popup detection...', 16, 'Some popup title');

sub Popup {
  my ($msg, $flags, $title) = @_;
  return Win32::MsgBox($msg, $flags, $title);
  die $msg;
}
[download]

Find the sample popup window:

# findpopup.pl
use Win32::GuiTest qw(:ALL :SW);

my @windows = FindWindowLike(0, 'Some popup title');

for my $win (@windows) {
      print "Found window $win with title '", GetWindowText($win), "'\
+n";
      my @children = GetChildWindows($win);
      for my $child (@children) {
        my $text = GetWindowText($child);
        next if ($text =~ /^\xff/); # you've found the icon
        next if ($text =~ /^OK|Cancel|Abort|Retry|Ignore|Yes|No$/); # 
+you've found a button
        print "Found child $child with text '$text'\n";
      }
      
}
[download]

I ran popup.pl from the desktop and opened a command prompt and ran findpopup.pl from there.

Output:
Found window 4036 with title 'Some popup title'
Found child 1444 with text 'testing popup detection...'

After running a couple tests this morning (I posted the node just before leaving work yesterday) I came to the same conclusion that it actually returned child and parent windows... I had no idea that a popup window was actually made of 2 windows - it seems awkward surely...
Thanks for your help !