Okay. Now you've shown us the sample config file, it shows that you are running each of multiple DEPLOY sections on each of the servers, each in a separate thread; hence your conflicts.

The simple solution to your problem is to only start one thread for each server; and call the deployRoutine() multiple times within that thread; serially.

Ie. Something like this:

foreach my $targetServer (@targets) {

    # Ping host to check its available
    my $p = Net::Ping->new();    
    if ($p->ping($targetServer)) {      

    my @subs; ### Accumulate the deployRoutines here

    foreach my $deploySection (@deployments) {  
        if ($flagDeploy) {

            my $deploySource = "$config{$deploySection}{'Source'}" ;
            my $deployDest = "$config{$deploySection}{'Destination'}" 
+;

            if ($flagNoMove) {

                ## Add this sub to the array to be executed for this s
+erver
                push @subs, sub { deployRoutine($targetServer, $deploy
+Source, $deployDest, "true") };          

                $threadDetails{$thread}{"Section"} = "$deploySection";
                $threadDetails{$thread}{"Target"} = "$targetServer";

            } else {

                ## Add this sub to the array to be executed for this s
+erver
                push @subs, sub { deployRoutine( $targetServer, $deplo
+ySource, $deployDest ) };          

                $threadDetails{$thread}{"Section"} = "$deploySection";
                $threadDetails{$thread}{"Target"} = "$targetServer";
            }
        }  
    }

    ## Now start one thread to execute them all; serially
    push @threads, threads->new( sub {
        $_->() for @subs;
    } );

    $p->close();
}
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Note: That is obviously untested code in the context of your application, but in isolation, the principle works:

{ 
    use threads;  
    my @subs = map{ eval "sub{ print $_; }" } 1 .. 10; 
    threads->new( sub{ $_->() for @subs; } ); 
    sleep 10; 
};;
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