Hi,
You are getting this warning because periodic conditions are implemented as a special case of the more general interface style boundary conditions, which allow one to connect two potentially different variables together at the boundaries.
This will not affect the solver at all, system transformation only provides capability for certain incompatible system forms to be transformed in to ones that MOL can deal with - if your system is already discretizing don’t worry, this won’t affect the result. I found it difficult to make this compatible with interfaces so added this check and warning to move forwards.
Can you post your full code related to MOL so I can take a look at why you’re getting all 0s?
PS A very well formatted and detailed question, good first post. Welcome to the community 