Some mods leave configuration files in your Saves folder. These aren't the mods themselves -- you'll note they aren't .package files or .ts4script file -- and the files can be left in even if you remove the mod. For example, Kuttoe's Home Regions mod leaves a .cfg (configuration) file there. Any info files a game leaves there can be safely deleted, but you'll have to redo your settings.
What happens if you do only a true vanilla (mod-free) test? See these instructions: https://answers.ea.com/t5/Mods-CC-Issues/INFO-How-to-Use-Mods-and-CC/m-p/13439356#TestVanilla
No instructions, by the way, require removing one file at a time to test. See 50-50 testing instead. And see also Broken/Updated Mods & CC.