Ah ok. The following should solve your problem, it is tested and works on my machine. Be sure to use a recent version of threads so that 'threads::running' and 'threads::joinable' are implemented.

while (@dirs_to_ftp) {
  my $dir= shift @dirs_to_ftp;
  startthread($dir);
  while (threads->list(threads::running)>=2) {
      sleep 1;
  }
  foreach my $thr (threads->list(threads::joinable)) {
      $thr->join();
  }
}

foreach my $thr (threads->list()) {
    $thr->join();
}
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