Ok, so after much frustration, learning a lot more than I wanted to know, and a lot of time tweaking, deleting, cache-clearing, saving, loading, reloading, searching forums, and rebooting, I think this is widely concerning the FPSC user community to warrant an official in-depth instruction for solving problems in the setup.ini.
It seems like people's most common issue is editing screen resolution.
The standard recommendation seems to be to make sure to close FPSC when making change to setup.ini.
But, the problem will reoccur because the change gets overwritten even if FPSC is closed.
Well, in my situation, there is a correct combination of lightmapping and advanced shading that looks perfect for the game(s) that I would like to create. I have created this appearance and recreated this appearance flawlessly a few times. But, when something happens that the settings gets changed, and I do not know what caused this, but it is nearly impossible to find a combination of events to correct the issue or get the right settings.
For me, I want to light and shade entities with nice ambient lighting and 3d shading without the extra post-process blur/shade/haze thing. Fog, shading, lighting, and reflective special effects were all working cohesively.
But, the preferences seem to overwrite the correct combination. There are more light map and shade options than there are preference combinations, and the combinations overwrite setup.ini even if the program is closed. In fact, deleting temp, using FPSCCleaner, rebooting, trying to save setup.init quickly during the process, etc. Somewhere in there, along with memorizing the right combination of control options, something works... it isn't a graphic card or drawing routine issue- or I would never have seen all the right options take place.
Just to rule out any other debugging stuff, I've tried with absolutely nothing booted, with lots of sound and graphic-type programs running in the background (I usually have wavelab and photoshop running in the background to edit the scene I am rendering, and this has been fine for the most part other than getting all visualizations at once- which is elusive until all prefs are tickable inside the program, save, and render.
Now, one person mentioned that perhaps the right combo only gets rendered in the build game, and then that is editable. Well, maybe that is the case- if that answers things that is awesome! Except, I have seen it work right in test mode. In fact, for hours on 3 separate occasions it was right in test mode. So, hmmm... again a little official support thread for getting settings that work- would save a few dozen people a lot of time I think.
Whatever the resolution is, it makes for a beautiful looking game!