I've actually gone and deleted the entirety of my mods list, and am in the process of building it back up. The difference this time: Mods were acquired EXCLUSIVELY through Nexus. My setup is almost finished, and none of the bugs previously encountered have occurred. In fact, New mods have been added without side effects. Which raises the question: Is there some form of 'disagreement' between the Nexus Mod Manager and the Bethesda modding interface?