When WPSC is activated or deactivated -but used in the past-, it can cause conflict with Affiliates. It can result in no referrals recorded and/or grant wrong affiliates with a referral.
In order to avoid this go to WP Super Cache settings under Advanced tab and enable the following option: Don’t cache pages with GET parameters. (?x=y at the end of a url).
Once this option is enabled, the affiliates system will work as it should.