Maybe you'd like to hear about this weird behaviour of wxlauncher I caught up lately, so I post it here. Please redirect me if necessary.
I wanted to use the [recommendedlighting] section of mod.ini file so I put this at the end of the file:
name = Jack's setup
flagset = -ambient_factor 100 -spec_exp 0.7 -spec_tube 1.0
Then in wxlauncher interface I could see my new preset line replacing the other one (baseline recommended) and when i selected it new settings appeared in "current command line" box.
But when I ran the game after this settings I could see no change in lightings. I know it could be very subtle changes at times so I dig further in this and I found out that cmdline_fso.cfg did not reflect my changes. Instead it had:
-ambient_factor 75 -spec_exp 11 -spec_tube 0.4
which are the exact settings you get when not using that mod.ini section! (or if one checks baseline recommended preset line)
To get it to work I had to copy my settings to custom flags box after choosing it in preset list (which automatically checks "Preset off"). This obviously makes mod.ini section useless, but I did get the good options in cmdline_fso.cfg and I could see changes in game too.
Hope this does not look like too confused explanations, I wish I could fix it by myself, but I can't