I've installed the new version of the affiliate plugin and setting it up to test.
All seems good but I've found a problem with the tracking of statistics.
In a different browser I've tested the affiliate urls and this is where the weirdness is.
In the admin login, it shows the clicks increment 1 by 1 as I test the url.
But when I login in (clean of cookies etc.. ) as a user on my multisite network their version of the stats show nothing.