Did you load from the main menu at any point (rather than the mods menu) and then save? That might cause an issue if Affects Saves Games is checked in the mod's properties--it's on by default, though not all mods need it. Maybe you can say which mods they are so it can be investigated.
I think I found the pattern if not the solution. It only seems to happen when the leader graphics are not loaded properly as well. I don't think it is mod specific. I will just be more careful with my saves.
Thanks
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