I've figured it out ... waitpid! *smacks own forehead*

This is causing execution to halt until the child process invoked by open3 has terminated. As such, the latter lines which read from the $STDOUT and $STDERR are not being executed until after child has terminated and thus delays between output on these handles cannot be appreciated. You will need to remove the waitpid statement if you want to read from these output streams while some_application is executed.