What string are you comparing? nbkid?? What does your input look like??

while(<FILE1>)  {
        chomp;
        my @fields = split(/:/, $_);
        my $result = qx{ /opt/bin/target -e$fields[2] };
        print FILE2 "$fields[0]:$fields[1]:$result:NONBKID\n";
        foreach my $configParameter (keys %{$configHash}) {
          my $nbkid = $configHash->{$configParameter}{'nbkid'};
          my $ntid = $configHash->{$configParameter}{'ntid'};

          if ($ntid eq $fields[1]) {
                print FILE2 "$fields[0]:$fields[1]:$result:$nbkid\n";
          } 
        }
}
[download]

change to

while(<FILE1>)  {
        chomp;
        my @fields = split(/:/, $_);
        my $result = qx{ /opt/bin/target -e$fields[2] };
        foreach my $configParameter (keys %{$configHash}) {
          my $nbkid = $configHash->{$configParameter}{'nbkid'};
          my $ntid = $configHash->{$configParameter}{'ntid'};

          if ($ntid eq $fields[1]) {
                print FILE2 "$fields[0]:$fields[1]:$result:$nbkid\n" i
+f $field[3] eq $nbkid;
        print FILE2 "$fields[0]:$fields[1]:$result:NONBKID\n" if $fiel
+d[3] ne $nbkid;

          } 
        }
}
[download]

maybe this is what you want? some of your information wasn't clear to me