I've just updated the Affiliate plugin to version 1.2.
There aren't many changes you will see in this version, but the backend of the plugin is moving towards a a more common affiliate framework for use in single and multi-site systems.
The main reason for releasing this update at this point is for the addition of a column in the multi-site systems super admin -> sites page.
This will highlight those blogs created from a referral and those that where then upgraded and is to make it easy to track down any issues that appear such as in this thread:
The column will look like the image below.
The update is available now from the usual place.