Maybe Net::FTP is unhappy?

use strict;
use warnings;
use Config;

BEGIN {
    $Config{useithreads}
        or die ('Recompile Perl with threads to run this program.');
};

use threads;

my $i = 0;
my $size = 200;
my $start_byte = 0;
my @THRD_LIST;
my $thrd;
my $targetSize = $size / 10;

while ($size) {
    my $chunk = $targetSize;
    
    $i++;
    $chunk = $size if $chunk > $size;
    $size -= $chunk;
    print "Process part $i. Size is $chunk\n";

    $thrd = threads->create (\&transfer_chunks, $i, $chunk)
        or die "Failed to start the thread: $@\n";
    push (@THRD_LIST, $thrd);
}

# start the threads
for $thrd (@THRD_LIST) {
    $thrd->join ();
}

print "All done\n";


sub transfer_chunks {
    my ($i, $chunk) = @_;

    while ($chunk--) {
        print "$i ";
        sleep 1 + rand (3);
    }
    
    print "\nprocess $i complete\n";
}
[download]

prints (for example):

Process part 1. Size is 4
1 Process part 2. Size is 4
Process part 3. Size is 4
2 Process part 4. Size is 4
3 Process part 5. Size is 4
4 Process part 6. Size is 4
5 Process part 7. Size is 4
6 Process part 8. Size is 4
7 Process part 9. Size is 4
8 Process part 10. Size is 4
9 10 1 3 4 5 6 10 3 4 8 9 2 3 6 7 8 10 1 5 7 8 9 
process 3 complete
4 10 2 
process 4 complete
6 1 5 7 
process 8 complete
9 2 
process 6 complete

process 9 complete

process 10 complete

process 1 complete

process 5 complete

process 7 complete

process 2 complete
All done
[download]

which is as expected on my XP system. Can you reproduce the problem without using FTP?