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Most likely, it's the last one. I have, had, and will continue to have a countless number of plugins installed, which I use to torment my poor Khajiit paladin. It should be noted that the save file with my second hero, where many plugins are disabled by default, runs, loads, and glitches much less.
I tried cleaning the save file with Wraith Bash, but either I'm not doing it right, or something is wrong with me; it doesn't help at all.