Try to put use strict; at the top of your script and always run it with the -w commandline switch. This often gives you a better idea of what *could be going wrong.
I ran you script like this and it didn't produce the error

use strict;
use vars qw($tmp_dir $dir);

open OUTPUTFILE, ">test.txt";

$tmp_dir = "test";
$dir = "tester";

if ($tmp_dir ne $dir) {
    print "dumping to file\n";
    print OUTPUTFILE "\n$tmp_dir\n";
    $dir = $tmp_dir;
}
[download]

Maybe there is something wrong in your assignment of $tmp_dir and $dir...

Jorg

"Do or do not, there is no try" -- Yoda