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All it will tell me is "Resource 086C is not loaded". I've uninstalled and reinstalled twice now and still no luck.
But usually, getting rid of everything solves this problem. Also deleting the kexengine.cfg and the mod.cfg in the AppData/Roaming/NightDive/System Shock EE folder will reset settings. But since you said you already deleted everything: I am sorry that I can't be of help beyond this point.