Since version 5+ Post Affiliate Pro stores all templates, images, CSS files in database instead of directly in file system.
In order to keep the link structure untouched (backward compatibility reasons) we have added a few rules to .htaccess files which redirect requests to correct files which load the requested resources from DB.
Also since version 126.96.36.199 we have added an extra option to hash names of tracking scripts which will work only in case of correct rewrite rules.
Since IIS doesn't support .htaccess files you have to add the rewrite rules from the following files to your ISS configuration:
/scripts/.htaccess (responsible for hashing of tracking scripts)
Windows-IIS server have built in utility for converting Apache htaccess rules to Windows-IIS rules. You can consult the official manual on this website http://www.iis.net/learn/extensions/url-rewrite-module/importing-apache-modrewrite-rules
For converting of rules may be also helpful this online converter: http://www.htaccesstowebconfig.com/
Another option might be to try 3rd party software Helicon Ape http://www.helicontech.com/ape/