The possible reasons for this are in the code you don't show. When you fork, you cannot know whether the child or parent runs first. If the parent runs first, and exits immediately, the child will be killed by the system's init process before it runs. Be sure to call wait() before exiting the parent. You should call exit() at the end of the child's code.

# create new directory here
if ( !defined( $pid = fork() ) ) {
   # log fork() failure here
   # remove directory here
}
elsif ($pid == 0) {
    # remove directory here
    exit 0;
}
wait if $pid;
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Update: Fixed pid logic according to dws's prescription

After Compline,
Zaxo