I currently have five different mods in my own MOD folder. None is being activated when using the new launcher (when unselected). You can always check which mods are active by starting the game, go to "Content" and select the "MOD" tab. Your mods should be listed there and stated if they are "Active" or "Inactive". Can you check which mods it is that is automatically loaded? Are these downloaded through Steam workshop or manually?
