I'll start by saying in hindsight its probably fairly obvious.
I was trying to be overly clever with my file naming and started to rename my entity type files as Entity.Contacts.pas etc. The issue appeared to be in the "Entity." bit.
My advice, DON'T name your files like this.
The compiler sees the Entity. as a file namespace and therefore started to ignore all the [Entity] attributes, which caused a major WTF moment. I have recently upgraded to 10.2 so I don't know if its a 10.2 feature only or not as I haven't tested on 10.1.or earlier but i suspect its just a Delphi thing.
Hope this helps someone avoid a similar facepalm moment.
Cheers
John.