Ok, here is the updated script. I can run it with the warnings on and get every single warning, but each system call is completing properly. Each status is being returned as 0. Very strange. If anyone can thing of something else to check on the system calls, I'd appreciate it.

use strict;
use warnings;
use Cwd;
use Getopt::Long;

my ($help) = 0;
my ($num) = 20;  # Number of loops to run
my ($testdir) = "";
my ($verbose) = 0;

GetOptions('help|?'    => \$help,
           "num=i"     => \$num,
           "testdir=s" => \$testdir,
           'verbose'   => \$verbose) or &usage();

&usage() if $help;

# Header
print "Beginning Directory Manipulation Testing...\n" if $verbose;
$| = 1;

# Get the current working directory
my $home_dir = getcwd;

# Change to the test directory
chdir($testdir) or die "Can't make $testdir: $!\n";

# Set up test dirs if they do not exist
if (!-d "test")
{
    mkdir("test") or die "Can't make $testdir\\test: $!\n";
}
if (!-d "test1")
{
    mkdir("test1") or die "Can't make $testdir\\test1: $!\n";
}

# Change to the test area
chdir("test") or die "Can't change to test directory: $!\n";

# Directory Manipulation
for (my $dir = 0; $dir < $num; $dir++)
{
    # Make the directory
    if (!-d "directory$dir" ) {
        mkdir("directory$dir", 0755) or die "Can't make $testdir\\test
+\\directory$dir: $!\n";
    }

    # Change permissions of the directory
    if ($^O =~ /Win32/)
    {
        print "\nRunning chmod from - $home_dir\\..\\..\\bin\\chmod on
+ $testdir\\test\\directory$dir.\n" if ($verbose);
        if ($verbose)
        {
            system($home_dir . "\\..\\..\\bin\\chmod -v a+rwx $testdir
+\\test\\directory$dir");
        }
        else
        {
            system($home_dir . "\\..\\..\\bin\\chmod a+rwx $testdir\\t
+est\\directory$dir");
        }
    }
    else
    {
        system("/bin/chmod 777 directory$dir");
          or warn "Could not chmod directory$dir: $?\n";
    }

    # Copy the directory
    if ($^O =~ /Win32/)
    {
        print "\nRunning $home_dir\\..\\..\\bin\\cp 
            on $testdir\\test\\directory$dir.\n" if ($verbose);
        system("$home_dir\\..\\..\\bin\\cp -rv directory$dir copieddir
+ectory$dir");
    }
    else
    {
        system("/bin/cp -r directory$dir copieddirectory$dir");
          or warn "Could not copy directory$dir to copieddirectory$dir
+: $?\n";
    }

    # Rename the directory
    if (!-d "copieddirectory$dir")
    {
        print "copieddirectory$dir does not exist!\n" if $verbose;
    }
    if ($^O =~ /Win32/)
    {
        system("move copieddirectory$dir ..\\test1\\moveddirectory$dir
+ > out.txt");
        if (-e "out.txt")
        {
            unlink("out.txt") or die "Can't unlink out.txt: $!\n";
        }
    }
    else
    {
        system("/bin/mv copieddirectory$dir ../test1/moveddirectory$di
+r");
          or warn "Could not move directory$dir to test1: $?\n";
    }

    # Delete the copied directory
    if ($^O =~ /Win32/)
    {
        rmdir("..\\test1\\moveddirectory$dir");
    }
    else
    {
        system("/bin/rm -r ../test1/moveddirectory$dir");
          or warn "Could not remove test1\\directory$dir: $?\n";
    }

    # Remove the directory
    if ($^O =~ /Win32/)
    {
        rmdir("directory$dir") or die "Can't remove directory: $!\n";
    }
    else
    {
        system("/bin/rm -r directory$dir");
          or warn "Could not remove directory$dir: $?\n";
    }
}

print "complete!\n" if ($verbose);
# Change back to the top directory
chdir($home_dir) or die "Can't move back to $home_dir: $!\n";

sub usage
{
    print "
$0 [options]

Options:
    -num          The number of loops to run, default $num
    -testdir      Location to run the test within
    -verbose      Run with messaging
    \n";
    exit(0);
}
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