but if I just click the .pl file it shuts down at the end.

Ah. That explains a great deal. If you really want/expect the script to work when it gets launched by clicking on the file's icon in a file browser, consider the following idiom:

#!/usr/bin/perl
# (use a unix/linux style shebang line,
# because someday you will want to use a unix/linux system)

use strict;

my $reqd_param_count = 2;  # (e.g. two file names)

if ( ! @ARGV ) {
    # prompt for interactive input of required parameter(s)
    ...
}
elsif ( @ARGV == $reqd_param_count ) {
    # invoked from an interactive shell: required params are in @ARGV
    ...
}
else {
    die "Usage:  $0  arg1 ...\n";
}
[download]

But seriously, there ought to be a sensible way to set things up so that a user can easily invoke a perl script with args (that will go into @ARGV). If not, just please switch to some sort of GUI approach (Tk, wx, etc), or else get cozy with using a CLI shell ("bash" is available for windows, and is the best, IMHO).