We have finally got all our problems sorted with the Mimecast Connector. For some reason we were getting an error when closing outlook:

The Error message I thought was referring to a third party plug-in in Outlook and in this case that plug-in was the Mimecast connector for Outlook. When I started Outlook with the Mimecast Connector disabled and then closed Outlook down it closed with no errors.
After spending lots of time on the phone with Mimecast and what seemed endless investigation into our Group Policies and Profiles it turned out that the error was actually being caused by a macro in Outlook that was used to call up a custom form.
So now we have finally got this sorted we are finally ready to push the connector to the rest of our Pilot users.
The latest version of the connector has the VC++ Runtime Libraries included with in the MSI file so it makes the push out a lot easier, all we need to do is assign a new package through GPO and push it down that way.
With the earlier versions of the deployment I pushed the user configuration details using the DeployMimecast.exe. This would allow me to specify the services we use, the user name and it then prompted the users to input their email address. so once they opened up outlook the Mimecast connector prompted the user for their AD Password.
However with the new version of the connector I noticed that just through opening up outlook once you had installed the Connector you were prompted for your email address, username and password. It automatically populates the services dependant on your domain, and that's it the user is now configured for the outlook connector, all he/she needs to do is restart outlook for the new account to take affect and then they are sorted.