After a lot of researching I have found out why it hadn't been working. The initial thread I was referring to was good for info but essentially too old and out of date. Please refer to this article from the MSDN Website:
http://msdn.microsoft.com/en-us/library/ee677285.aspx
Essentially, I had all my sites and services, in IIS, set up as a "Web Site". When you goto the WCF & WF Configuration set up, inside it does not contain an option saying "Auto-Start". What you have to actually do is setup the Service as an "Application" under a Web Site in IIS. Once you set it up, return to the WCF and WF Configuration and you will then see an "Auto-Start" option available in the list on the left hand side. The default value is "Disabled", simply "Enable" this and click Apply - it will need to refresh the service then you are good to go.
In addition, endpoint url's in your web.config will need to be updated e.g. localhost:8099/Service1.xamlx becomes localhost:8099/ServiceApplication/Service1.xamlx