The problem with using multiple mods at once is that some data and/or values MIGHT conflict with one another since default xml reference files could try accessing the same resources for a feature while modded elements can only be active from their unique processes.
You may also have had the 'directory listing' bug where the mod lines aren't written up in the popup which would confuse users as to what is currently valid, thus the impression that the settings are flawed.
One trick i found useful to prevent that sort of stuff is to maintain an "all empty default" folder which must be loaded (temporarily) between game sessions to reset things, so to speak.
Once the activate button is ticked (to use other but properly defined mod folders), the initialization settings are created from a clean slot dataset rather than 'doubling' some elements from the regular default directory (if it so happens that there ARE values or items loading from it or saved up ini files).
It's always a good idea to reset everything off simply by starting 'clean' anyway.
