The way some constants are currently declared and used, the only way to change their default values is to comment/uncomment their declaration in affiliateincludes/includes/config.php, which causes an issue when upgrading the plugin to new versions. So please at least allow us to re-declare them in wp-config.php thanks to the following changes:
if(defined('AFFILIATE_CHECKALL') && AFFILIATE_CHECKALL == 'yes')
if(defined('AFFILIATE_SETNOCOOKIE') && AFFILIATE_SETNOCOOKIE == 'yes')
5 occurrences for the first one and 1 occurrence on line 311 of affiliate.php for the second one.
Even better: include the config file from an action hook rather than directly on loading the plugin so we can re-declare the constants in a plugin or a theme instead of the wp-config.php file.