Just to follow this up. This morning I'm not having these problems but nothing has changed code wise. I'm happy its fixed its self but slightly worried I have no idea why.
EDIT:
On further investigation this still happens for me but only on 'dev shops'. When creating a dev shop I choose 'building a store for a client' and I can replicate this behaviour. If I create a store as 'test shop for apps', this does not happen. Possibly a bug?