Pro Sites: plugin control has gone missing


I have a pro site setup, the ability to control which plugins are on which site level is great.

However, since we made some changes, the link to manage which plugins are on which level has disappeared.

Initially it disappeared on my colleagues local setup right from when he first copied the site over from our live setup to his local.

We have now run a script on the live DB to change the domain name we were setup on, and we have added Easy Blogging, and the link to plugins from pro sites has disappeared there too.

Any ideas?