Yeah, that could be any number of things...all resulting in, most likely, a borked save file. Whether it's an update causing a latent version with the trainer, or the save file having present issues with the mods, or a weird issue with the basic system purely in vanilla, there's no surefire way to say, now.
My best recommendation would be to take it up in the Mods pages. Someone there may recognize what you're seeing.
If not...it's probably begin-a-new-game time. Once a save file is saved with mods running, it's modded forever, for better or worse.