Missing Shadows on Some Objects

For some reason real-time shadows are missing on some objects and and fine on others. This issue does not happen when in scene view.

I have been trying to figure out what's going on and figured out its only happening when I have multiple scenes being built in the output. It is also dependant on the order of scenes.

This screams to me that this is a genuine 'bug' rather than 'user error'.

If it makes any difference I am using the Legacy Deferred (light prepass) rendering path. I am using 100% real-time shadows, nothing is baked in any scenes. I'm using Unity 5.1.

Any help greatly appreciated.

Regards:

John