About the masked textures: you can have textures which are set as masked, and surfaces which are set as masked. If either is set as masked, you will see a masked texture in the editor (and in-game most of the time).
I think you can only avoid problems if you have both the texture *and* the surface set as masked (which can be easy to forget to do as you're applying masked textures in-editor). One solution - when your map is finished, select all surfaces by texture for the masked textures, then set the masked surface flag.
I hope that makes sense to/helps someone.