Lightmap system is fundamentally broken in Unity 5

I've had nothing but negative experiences with lightmapping ever since Unity 5. Something is fundamentally broken with it as map breaking lighting bugs can be triggered for literally no reason.

Realtime

Baked

If all lighting is realtime it works, and on new scenes it will initially work fine, but eventually something like this will start happening for no reason. Sometimes without any changes being made in the scene.

I sent a bug report with an example scene to Unity themselves and they replied saying they weren't sure what caused the problem and that I should update Unity. Unsurprisingly after completely unistalling Unity, installing the latest version and waiting for the project to update, I was still left with this problem.

This can happen on any project I have so it's not just exclusive to this one. There are no error messages in the console and I have no idea what to do. I'm willing to try any suggestions you may have to try and fix this.