I am using Poser 12. For as long as I have used Poser, I have always gone to the File Menu and selected Save or Save As. Never had an issue until these two instances, as far as I know. Although I don't often go back and open scenes once I've finished and rendered. I don't encounter any dialogue box either when I use Save or Save as, that's why I'm surprised it only save a partial scene.

I did ultimately save my Material Pose for Michael to the material room. I am using Superfly to render. I am attaching my water setup.

The first time I saved the Scene (File\Save) I had this setup. Later in the day when I re-opened the scene to continue my work, the two nodes were gone.  The only thing that showed was the PoserSurface panel. 

And I think I just solved this mystery. Apparently when I was creating the original shader, I had the ground selected and not the square which was the "water."