In the end I 'hacked' it by creating a different root object and parent my model to that. With that it worked fine.
I'd say there is definitely some issues with the scene graph. As well as the above issue, these things also happened seemingly overnight:
1. I had a hierarchy which was being created perfectly. I saved everything, went to bed and in the morning after restarting C3 only the parent object was being created and it was also scaled up.?!? The code was/is exactly the same as yesterday.
2.I created a hierarchy in one layout and then created it in code in another..once it came in WITH its tween behaviour (but this was scaled much bigger than on the initial sheet) but after restarting C3 the next day it comes in with no tweening at all.
As far as I can tell there was no update this morning but maybe C3 updated itself during this time? I'm running r295 Beta