Hi Bruce,
I can certainly understand your frustration, but we can leave that for another topic. Instead I can try to help you try and detect what or where the issue may be. We had a similar issue and the method we use seems to have helped. Mind you, we are still running v1.17 of FPSC using our own
in-house modded version, but perhaps our method may help you.
First off, there are the two methods to changing the skybox as you pointed out. One is in the editor's build level setup, and the second is the manual method. In the editor's build setup, there is that part where you can create a game project file. That project creates the "fpg" file and that file also creates a folder with the fpi files it requires (gameover, gamewon, loadingpage, setuplevel, and titlepage).
Recall that during a test game, the test will use the files from the "languagebank\english\gamebank\mylevel" folder. We set our skybox up manually in there to test our level. When we created the project file, we will copy those fpi files into our project folder. We do this for each level we make. If you open that project fpg using notepad, you can see how the structure is and it points to all the required folders, etc for that project. When we build, we ensure that the fpi files I mentioned earlier are in our project folder and we select it before we build. Perhaps checking to see which project file you are working with and viewing that fpg file to ensure you edited the correct file for the skybox.
In your case, what happens when you make a build? In other words, let's suppose you make a project file name, which will use the "languagebank\english\gamebank\YOURPROJECTNAME" folder. You edit that setuplevel.fpi to reflect on the skybox you want, then run a build. Does the skybox appear properly at that point? If not, check the build and copy the skybox to the skybank folder, then edit the setuplevel.fpi file in your build. does it work then?
By the software's current design, you can do a build with a skybox and change it at any time- all by editing that setuplevel.fpi file and then copying the skybox to its proper location in the build. So I can build a game level using the default "gas" and then switch it to something else, providing I copy the skybox to the skybank folder and edit my setuplevel.fpi file. If it still is not doing it for you at that point, then it could be another issue that is affecting you.

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