my $oldfh = select STDERR;
    local $| = 1;
    select $oldfh;
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This is superfluous as the STDERR stream is unbuffered.

    my $run = "perl /webRoot/apps/startPipe.pl -f $dest_file -j $job_ 
++ID -c $created -t $job_type $adv_opts"; `$run`;
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You have forked a new process and now you are using backticks in void context which forks another process and starts a shell to run your command and returns the STDOUT of that command. Just use exec:

    exec 'perl', '/webRoot/apps/startPipe.pl', '-f', $dest_file, '-j',
+ $job_', '+ID', '-c', $created, '-t', $job_type, $adv_opts;
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