First of all, if you want to upgrade never make a new installation, do not run install.php!

Please make sure that you have a complete database backup before you upgrade. I also recommend that you backup your old files.

Upgrade from version 1.0.0x to 1.0.1:
This update of iRedirector Subdirectory Edition brings you all the great Subdomain Edition 1.0.6 features including a new template system and language file system. To update: Please make sure to replace ALL files including ALL templates and even the config.php. The best way to do this update is do backup the old files first, then delete them from the server and upload the new ones. Make sure to use the MySQL login you used before and run upgrade1.php.

Now edit your redir.php:
Replace:

if (!defined('directory')) { 
define('directory', ''); 
}

if (!defined('directory')) { 
define('directory', '/FULL/PATH/TO/YOUR/INSTALLATIONFOLDER/'); 
}