It seems to me that the debugger would lose some utility if it printed all its output to a log. Anyhow...

You might try localizing the handles,

{
    open local(*STDOUT), "> $log" or die $!;
    open local(*STDERR), ">>&STDOUT" or die $!;
    flock(STDOUT, LOCK_EX | LOCK_NB) or die $!;
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Why do you use non-blocking? That will cause you to exit instead of waiting until the file is available. I also don't see why you need truncate, following. You already clobbered the old log when you opened STDOUT.

    truncate STDOUT, 0; #clear out STDOUT to start with a fresh log fi
+le.
    chdir $local_dir or die "Cannot change to $local_dir. $!";
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I don't know whether $pkunzip makes use of the current directory, but it wouldn't hurt to use Cwd 'chdir'; before this, so that directory changes get into the child's environment.

    system $pkunzip, '-doA', "$local_dir/$file";
}
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I rewrote the system call to avoid going through the shell. You'll need to call glob yourself if you've been relying on the shell to expand file names to a list.