Has anyone else had a problem with the computational domain or meshing after cloning a project?

I've had this a couple of times now on different models, after running a project I clone it and change a boundary condition value, e.g. increase a mass flow rate, then try to re run it. When it tries to mesh it doesn't seem to see the model and just meshes the entire domain as fluid. If I then change the computational domain slightly (make it slightly larger in one dimension, save it, then reset it) it then meshes properly again.

Any ideas what is causing this?