I have had a similar thing happen with CCR .toml files that use the 'SaveINIFiles' command after one or more 'SetINISetting' commands. In my case I am using Mod Organizer 2, and an .ini file was being generated in the Overwrite folder, but it would be named after the last .esp/,esm in my plugin list. So this has nothing to do with the actual .esp/.esm mod that the generated .ini is named after. Through "trial and error" and testing other .toml mods, I discovered that the 'SaveINIFiles' command doesn't seem to be needed for the 'SetINISetting' commands to have an effect.