I've just released version 2.4.2 of the affiliate plugin. This version has a couple of fixes as well as some new functionality related to advanced affiliate settings.
Updated translation file - if you are working on a translation for the plugin, can you ensure that you use this .po / .mo file as your base.
IE9 cookie retention - IE9 had a habit of not retaining affiliate cookies, this version fixes that issue.
The advanced affiliate settings allows a user to enter a URL in their profile and any referrals from that URL will be counted as clicks for that user. This new version highlights any users that has that option set in the affiliate admin area, as well as introduces a "validation" procedure to ensure that the user actually "owns" or has some control over the URL they are entering (think google webmaster tools).
To enable this new option you can either edit the config.php file (in affiliateincludes/includes) and set the option AFFILIATE_VALIDATE_REFERRER_URLS to 'yes' or add the following line to your wp-config.php file