I use about 50 mods at any given time, mostly because the gun mods that I use aren't bundled together. I've noticed that, when I start a new game, most of the mods that I selected for that game are no longer active. Most mods that I use can be activated during a new game, but not certain ones, like SIS Team Start. I have to have that one active when the game begins, or it doesn't work for painfully obvious reasons, but it is sometimes among those no longer active, meaning that I have to start an entirely new game from scratch. My workaround is to only activate those that have to be active at game's start, then activate the rest once the game begins. However, aside from important mods not being activated when I start, the game also deactivates a number of those that I've now activated after the game starts. Because of this, I have to select a few, go back to the pause menu, then back into the active mod list, and activate more. I always have to reactivate a few that I just activated, so it takes a while.

Should I be using a mod organizer instead? Any help would be appreciated.