Your first version of code with the excellent suggestion from BrowserUK looks like it should work. What may be happening here is that the windows you put up are just info info windows and re-display of these windows happens so fast that you don't notice it before program ends.

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]

This segment of code will cause a "block" until user hits the OK button, ie program hangs until user does something. So presumably whatever you've already got up there will stay up there.