You might be creating strawmen ( relatives of zombies), as ikegami pointed out in Re^3: Stopping subprocesses

That is the first time I've seen the strawman behavior, it's like grandchildren that won't die as part of a kill command. Only saving the pid of the command or it's associated shell, and killing it's pid will clean them up.

As you switch from backticks, to a form of IPC that gives the pid, have your slave threads either kill the pid themselves before joining(ending), or have them stuff the pid into a thread shared variable, so the master thread can do the cleanup.

In my experience, I always use Proc::Killfam on the pid obtained in the slave thread, since it will kill the shell and program pid.