Pro Sites problem with new user activation

Hi I'm using the latest version of Pro Sites. When a user of a site creates another user in their site they are sent an activation email but the link in the email is wrong and goes to a 404.

In the activation email the link is like http://mainsite.com/subsite/wp-activate.php?key=40bd161cc316ddfd

What it should be is

http://mainsite.com/wp-activate.php?key=40bd161cc316ddfd

If I manually change it in the browser it works...

I'm using Prosites set up with sites being in subdirectories and then using the domain mapping plugin to map domains to the subsite.

Help!