Could you try running this and let me know if it functions properly. I combined a few subs and eliminated the delete sub. But I wasn't sure how to test it.

#!/usr/bin/perl

use strict;
use warnings;
use File::Copy;

sub copy_from_root {
    my $ftp_dir = shift;
    opendir my $dir, $ftp_dir or die "Cannot open $ftp_dir: $!";
    my %short_names;
    for my $file_name (grep /\.(?:txt|doc|mpd|mta)$/i, readdir $dir) {
        my $daym = (localtime)[3];
        my @dirs = ("c:/afis3too/$daym", 'c:/scripts/attempt', 'c:/rep
+orts');
        print $file_name;
        chomp $file_name;
        my $source = "$ftp_dir/$file_name";
        $short_names{sprintf('%.6s.bat', lc $file_name)}++;
        if ($file_name =~ /^(?:afinv|csinv|sfinv)/i) {
            s/\.mta$/\.mpd/i;
            push @dirs, 'c:/invoice';
        } elsif ($file_name =~ /\.doc$/i) {
            s/doc$/txt/ig;
        } elsif ($file_name =~ /\.mta$/i) {
            s/mta$/mpd/ig;
        }
        foreach my $dir (@dirs){
            copy($source, "$dir/$file_name") or
                 die "Cannot copy $dir/$file_name: $!";
        }
        unlink $source or die "Cannot unlink $source: $!";
    }
    return keys %short_names;
}

sub batch_files {
    my $batch_dir = shift;
    opendir my $dir, $batch_dir or die "Cannot open $batch_dir: $!";
    my @files = grep /\.bat$/i, readdir $dir;
    return \@files;
}

sub run_the_batches {
    my ($short_names, $batch_files, $dir) = @_;
    my @matches;
    foreach my $short_name (@$short_names){
        push @matches, grep /$short_name$/i, @$batch_files;
        print "Working...\n";
    }
    system("$dir/$_") for @matches;
}


my $ftp_dir         = 'c:/ftproot';
my $report_dir      = 'c:/reports';

print "\n\n\n";
print "         Robco Inc. Presents :   \n\n\n";
print "     The NEW, AMAZING, INCREDIBLE ....\n\n\n";
print "      Robco Document Rotisserie!!!!!\n\n\n";
print "Just RENDER it, THEN don't REMEMBER it!!!!!\n\n";
print "         It's just that easy.\n\n\n\n\n";

while (1) {
    print localtime, "\n";
    print "sleeping ....  ZzZzZzZzZz......\n";
    sleep (10);
    print "OK! OK!  ....  I'm awake!  ....  I'm awake\n";

    my $short_names = copy_from_root($ftp_dir);
    my $batch_files = batch_files($report_dir);
    run_the_batches($short_names, $batch_files, $report_dir);
}
[download]

As mentioned above, I am unsure how to test all my changes. I'm sure there's a glitch or two.